1QKI: Human glucose 6-phosphate dehydrogenase
X-ray structure of human glucose 6-phosphate dehydrogenase (variant canton R459L) complexed with structural NADP+. Determined by X-ray diffraction at 3.0 Å resolution. Released 16 Mar 2000.
- Method
- X-ray diffraction
- Resolution
- 3.0 Å
- Organism
- HOMO SAPIENS
- Chains
- 8
- Atoms
- 31,663
- Mol. weight
- 480.36 kDa
- Ligands
- GOA, NAP
- Released
- 16 Mar 2000
Explore 1QKI in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
1QKI contains 240 α-helices and 146 β-strands across 8 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain A: 30 helices, 20 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 32-37 | 6 | 1 |
| α-helix | 42-43 | 2 | |
| α-helix | 44-48 | 5 | |
| α-helix | 49-57 | 9 | |
| β-strand | 65-70 | 6 | 1 |
| β-strand | 71 | 1 | 2 |
| α-helix | 78-84 | 7 | |
| α-helix | 92-94 | 3 | |
| α-helix | 95-102 | 8 | |
| β-strand | 105-106 | 2 | 1 |
| β-strand | 109 | 1 | 2 |
| α-helix | 115-127 | 13 | |
| β-strand | 135-140 | 6 | 1 |
| α-helix | 144-157 | 14 | |
| β-strand | 165-169 | 5 | 1 |
| α-helix | 177-190 | 14 | |
| α-helix | 193-195 | 3 | |
| β-strand | 196-198 | 3 | 1 |
| α-helix | 201-204 | 4 | |
| α-helix | 206-216 | 11 | |
| β-strand | 230-238 | 9 | 3 |
| α-helix | 247-250 | 4 | |
| α-helix | 254-255 | 2 | |
| α-helix | 256-264 | 9 | |
| α-helix | 265-272 | 8 | |
| α-helix | 273-276 | 4 | |
| α-helix | 281-292 | 12 | |
| β-strand | 295 | 1 | 4 |
| α-helix | 296-299 | 4 | |
| α-helix | 300-302 | 3 | |
| β-strand | 303-309 | 7 | 3 |
| α-helix | 316-319 | 4 | |
| β-strand | 337-343 | 7 | 3 |
| β-strand | 344 | 1 | 4 |
| β-strand | 353-359 | 7 | 3 |
| β-strand | 366-373 | 8 | 3 |
| α-helix | 374-376 | 3 | |
| β-strand | 389-395 | 7 | 3 |
| β-strand | 399-407 | 9 | 3 |
| α-helix | 408 | 1 | |
| β-strand | 415-423 | 9 | 3 |
| α-helix | 424-427 | 4 | |
| α-helix | 431-435 | 5 | |
| α-helix | 436-446 | 11 | |
| α-helix | 449-451 | 3 | |
| β-strand | 453 | 1 | 1 |
| α-helix | 455-475 | 21 | |
| α-helix | 477-479 | 3 | |
| β-strand | 480-483 | 4 | 3 |
| α-helix | 490-498 | 9 | |
Chain B: 31 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 32-37 | 6 | 5 |
| α-helix | 42-43 | 2 | |
| α-helix | 44-48 | 5 | |
| α-helix | 49-57 | 9 | |
| β-strand | 65-71 | 7 | 5 |
| α-helix | 78-81 | 4 | |
| α-helix | 92-94 | 3 | |
| α-helix | 95-102 | 8 | |
| β-strand | 105-109 | 5 | 5 |
| α-helix | 115-127 | 13 | |
| β-strand | 135-140 | 6 | 5 |
| α-helix | 144-153 | 10 | |
| α-helix | 154-158 | 5 | |
| β-strand | 165-169 | 5 | 5 |
| α-helix | 179-187 | 9 | |
| α-helix | 193-195 | 3 | |
| β-strand | 196-198 | 3 | 5 |
| α-helix | 201-204 | 4 | |
| α-helix | 206-216 | 11 | |
| β-strand | 230-238 | 9 | 3 |
| α-helix | 247-250 | 4 | |
| α-helix | 254-255 | 2 | |
| α-helix | 256-264 | 9 | |
| α-helix | 265-272 | 8 | |
| α-helix | 273-276 | 4 | |
| α-helix | 281-292 | 12 | |
| β-strand | 295 | 1 | 6 |
| α-helix | 296-299 | 4 | |
| α-helix | 300-302 | 3 | |
| β-strand | 303-309 | 7 | 3 |
| α-helix | 316-319 | 4 | |
| β-strand | 337-343 | 7 | 3 |
| β-strand | 344 | 1 | 6 |
| β-strand | 353-359 | 7 | 3 |
| β-strand | 366-373 | 8 | 3 |
| α-helix | 374-376 | 3 | |
| β-strand | 389-395 | 7 | 3 |
| β-strand | 399-407 | 9 | 3 |
| α-helix | 408 | 1 | |
| β-strand | 415-423 | 9 | 3 |
| α-helix | 424-427 | 4 | |
| α-helix | 431-435 | 5 | |
| α-helix | 436-446 | 11 | |
| α-helix | 449-451 | 3 | |
| β-strand | 453 | 1 | 5 |
| α-helix | 455-475 | 21 | |
| α-helix | 477-479 | 3 | |
| β-strand | 480-483 | 4 | 3 |
| α-helix | 490-498 | 9 | |
Chain C: 30 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 31-37 | 7 | 7 |
| α-helix | 42-43 | 2 | |
| α-helix | 44-48 | 5 | |
| α-helix | 49-57 | 9 | |
| β-strand | 64-71 | 8 | 7 |
| α-helix | 77-81 | 5 | |
| α-helix | 92-94 | 3 | |
| α-helix | 95-102 | 8 | |
| β-strand | 105-109 | 5 | 7 |
| α-helix | 115-127 | 13 | |
| β-strand | 135-140 | 6 | 7 |
| α-helix | 144-153 | 10 | |
| α-helix | 154-158 | 5 | |
| β-strand | 165-169 | 5 | 7 |
| α-helix | 177-188 | 12 | |
| α-helix | 193-195 | 3 | |
| β-strand | 196-198 | 3 | 7 |
| α-helix | 201-204 | 4 | |
| α-helix | 206-216 | 11 | |
| β-strand | 230-238 | 9 | 8 |
| α-helix | 247-250 | 4 | |
| α-helix | 254-255 | 2 | |
| α-helix | 256-264 | 9 | |
| α-helix | 265-272 | 8 | |
| α-helix | 273-276 | 4 | |
| α-helix | 281-292 | 12 | |
| β-strand | 295 | 1 | 9 |
| α-helix | 296-299 | 4 | |
| α-helix | 300-302 | 3 | |
| β-strand | 303-309 | 7 | 8 |
| α-helix | 316-319 | 4 | |
| β-strand | 337-343 | 7 | 8 |
| β-strand | 344 | 1 | 9 |
| β-strand | 353-359 | 7 | 8 |
| β-strand | 366-373 | 8 | 8 |
| α-helix | 374-376 | 3 | |
| β-strand | 389-395 | 7 | 8 |
| β-strand | 399-407 | 9 | 8 |
| β-strand | 415-423 | 9 | 8 |
| α-helix | 424-427 | 4 | |
| α-helix | 432-435 | 4 | |
| α-helix | 436-446 | 11 | |
| α-helix | 449-451 | 3 | |
| β-strand | 453 | 1 | 7 |
| α-helix | 455-475 | 21 | |
| α-helix | 477-479 | 3 | |
| β-strand | 480-483 | 4 | 8 |
| α-helix | 490-499 | 10 | |
Chain D: 30 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 32-37 | 6 | 10 |
| α-helix | 42-43 | 2 | |
| α-helix | 44-48 | 5 | |
| α-helix | 49-57 | 9 | |
| β-strand | 65-71 | 7 | 10 |
| α-helix | 77-81 | 5 | |
| α-helix | 92-94 | 3 | |
| α-helix | 95-102 | 8 | |
| β-strand | 105-109 | 5 | 10 |
| α-helix | 115-127 | 13 | |
| β-strand | 135-140 | 6 | 10 |
| α-helix | 144-153 | 10 | |
| α-helix | 154-158 | 5 | |
| β-strand | 165-169 | 5 | 10 |
| α-helix | 177-190 | 14 | |
| α-helix | 193-195 | 3 | |
| β-strand | 196-198 | 3 | 10 |
| α-helix | 201-204 | 4 | |
| α-helix | 206-216 | 11 | |
| β-strand | 230-238 | 9 | 8 |
| α-helix | 247-255 | 9 | |
| α-helix | 256-264 | 9 | |
| α-helix | 265-272 | 8 | |
| α-helix | 273-276 | 4 | |
| α-helix | 281-292 | 12 | |
| β-strand | 295 | 1 | 11 |
| α-helix | 296-299 | 4 | |
| α-helix | 300-302 | 3 | |
| β-strand | 303-309 | 7 | 8 |
| α-helix | 316-319 | 4 | |
| β-strand | 337-343 | 7 | 8 |
| β-strand | 344 | 1 | 11 |
| β-strand | 353-359 | 7 | 8 |
| β-strand | 366-373 | 8 | 8 |
| α-helix | 374-376 | 3 | |
| β-strand | 389-395 | 7 | 8 |
| β-strand | 399-407 | 9 | 8 |
| α-helix | 408 | 1 | |
| β-strand | 415-423 | 9 | 8 |
| α-helix | 424-427 | 4 | |
| α-helix | 432-435 | 4 | |
| α-helix | 436-446 | 11 | |
| α-helix | 449-451 | 3 | |
| β-strand | 453 | 1 | 10 |
| α-helix | 455-475 | 21 | |
| α-helix | 477-479 | 3 | |
| β-strand | 480-483 | 4 | 8 |
| α-helix | 490-499 | 10 | |
Chain E: 30 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 31-37 | 7 | 12 |
| α-helix | 42-43 | 2 | |
| α-helix | 44-48 | 5 | |
| α-helix | 49-57 | 9 | |
| β-strand | 64-71 | 8 | 12 |
| α-helix | 92-94 | 3 | |
| α-helix | 95-104 | 10 | |
| β-strand | 105-109 | 5 | 12 |
| α-helix | 115-127 | 13 | |
| β-strand | 135-140 | 6 | 12 |
| α-helix | 144-153 | 10 | |
| α-helix | 154-158 | 5 | |
| β-strand | 165-169 | 5 | 12 |
| α-helix | 178-190 | 13 | |
| α-helix | 193-195 | 3 | |
| β-strand | 196-198 | 3 | 12 |
| α-helix | 201-204 | 4 | |
| α-helix | 206-216 | 11 | |
| β-strand | 230-238 | 9 | 13 |
| α-helix | 247-250 | 4 | |
| α-helix | 254-255 | 2 | |
| α-helix | 256-264 | 9 | |
| α-helix | 265-272 | 8 | |
| α-helix | 273-276 | 4 | |
| α-helix | 281-292 | 12 | |
| β-strand | 295 | 1 | 14 |
| α-helix | 296-299 | 4 | |
| α-helix | 300-302 | 3 | |
| β-strand | 303-309 | 7 | 13 |
| α-helix | 316-319 | 4 | |
| β-strand | 337-343 | 7 | 13 |
| β-strand | 344 | 1 | 14 |
| β-strand | 353-359 | 7 | 13 |
| β-strand | 366-373 | 8 | 13 |
| α-helix | 374-376 | 3 | |
| β-strand | 389-395 | 7 | 13 |
| β-strand | 399-407 | 9 | 13 |
| α-helix | 408 | 1 | |
| β-strand | 415-423 | 9 | 13 |
| α-helix | 424-427 | 4 | |
| α-helix | 431-435 | 5 | |
| α-helix | 436-446 | 11 | |
| α-helix | 449-451 | 3 | |
| β-strand | 453 | 1 | 12 |
| α-helix | 455-475 | 21 | |
| α-helix | 477-479 | 3 | |
| β-strand | 480-483 | 4 | 13 |
| α-helix | 490-499 | 10 | |
Chain F: 29 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 31-37 | 7 | 15 |
| α-helix | 42-43 | 2 | |
| α-helix | 44-48 | 5 | |
| α-helix | 49-57 | 9 | |
| β-strand | 64-71 | 8 | 15 |
| α-helix | 81-84 | 4 | |
| α-helix | 92-94 | 3 | |
| α-helix | 95-102 | 8 | |
| β-strand | 105-109 | 5 | 15 |
| α-helix | 115-127 | 13 | |
| β-strand | 135-140 | 6 | 15 |
| α-helix | 144-153 | 10 | |
| α-helix | 154-158 | 5 | |
| β-strand | 165-169 | 5 | 15 |
| α-helix | 177-187 | 11 | |
| α-helix | 193-195 | 3 | |
| β-strand | 196-198 | 3 | 15 |
| α-helix | 201-204 | 4 | |
| α-helix | 206-216 | 11 | |
| β-strand | 230-238 | 9 | 13 |
| α-helix | 247-255 | 9 | |
| α-helix | 256-264 | 9 | |
| α-helix | 265-272 | 8 | |
| α-helix | 273-276 | 4 | |
| α-helix | 281-292 | 12 | |
| β-strand | 295 | 1 | 16 |
| α-helix | 296-299 | 4 | |
| α-helix | 300-302 | 3 | |
| β-strand | 303-309 | 7 | 13 |
| α-helix | 316-319 | 4 | |
| β-strand | 337-343 | 7 | 13 |
| β-strand | 344 | 1 | 16 |
| β-strand | 353-359 | 7 | 13 |
| β-strand | 366-373 | 8 | 13 |
| α-helix | 374-376 | 3 | |
| β-strand | 389-395 | 7 | 13 |
| β-strand | 399-407 | 9 | 13 |
| β-strand | 415-423 | 9 | 13 |
| α-helix | 424-427 | 4 | |
| α-helix | 432-435 | 4 | |
| α-helix | 436-445 | 10 | |
| α-helix | 449-451 | 3 | |
| β-strand | 453 | 1 | 15 |
| α-helix | 455-475 | 21 | |
| α-helix | 477-479 | 3 | |
| β-strand | 480-483 | 4 | 13 |
| α-helix | 490-499 | 10 | |
Chain G: 29 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 31-37 | 7 | 17 |
| α-helix | 42-43 | 2 | |
| α-helix | 44-48 | 5 | |
| α-helix | 49-57 | 9 | |
| β-strand | 64-71 | 8 | 17 |
| α-helix | 75-77 | 3 | |
| α-helix | 78-81 | 4 | |
| α-helix | 92-94 | 3 | |
| α-helix | 95-102 | 8 | |
| β-strand | 105-109 | 5 | 17 |
| α-helix | 115-127 | 13 | |
| β-strand | 135-140 | 6 | 17 |
| α-helix | 144-157 | 14 | |
| β-strand | 165-169 | 5 | 17 |
| α-helix | 177-190 | 14 | |
| β-strand | 196-198 | 3 | 17 |
| α-helix | 201-204 | 4 | |
| α-helix | 206-216 | 11 | |
| β-strand | 230-238 | 9 | 18 |
| α-helix | 247-250 | 4 | |
| α-helix | 254-255 | 2 | |
| α-helix | 256-264 | 9 | |
| α-helix | 265-272 | 8 | |
| α-helix | 273-276 | 4 | |
| α-helix | 281-292 | 12 | |
| β-strand | 295 | 1 | 19 |
| α-helix | 296-299 | 4 | |
| α-helix | 300-302 | 3 | |
| β-strand | 303-309 | 7 | 18 |
| α-helix | 316-319 | 4 | |
| β-strand | 337-343 | 7 | 18 |
| β-strand | 344 | 1 | 19 |
| β-strand | 353-359 | 7 | 18 |
| β-strand | 366-373 | 8 | 18 |
| α-helix | 374-376 | 3 | |
| β-strand | 389-395 | 7 | 18 |
| β-strand | 399-407 | 9 | 18 |
| β-strand | 415-423 | 9 | 18 |
| α-helix | 424-427 | 4 | |
| α-helix | 432-435 | 4 | |
| α-helix | 436-446 | 11 | |
| α-helix | 449-451 | 3 | |
| β-strand | 453 | 1 | 17 |
| α-helix | 455-475 | 21 | |
| α-helix | 477-479 | 3 | |
| β-strand | 480-483 | 4 | 18 |
| α-helix | 490-499 | 10 | |
Chain H: 31 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 32-37 | 6 | 20 |
| α-helix | 42-43 | 2 | |
| α-helix | 44-48 | 5 | |
| α-helix | 49-57 | 9 | |
| β-strand | 65-71 | 7 | 20 |
| α-helix | 78-84 | 7 | |
| α-helix | 92-94 | 3 | |
| α-helix | 95-102 | 8 | |
| β-strand | 105-109 | 5 | 20 |
| α-helix | 115-127 | 13 | |
| β-strand | 135-140 | 6 | 20 |
| α-helix | 144-153 | 10 | |
| α-helix | 154-158 | 5 | |
| β-strand | 165-169 | 5 | 20 |
| α-helix | 177-188 | 12 | |
| α-helix | 193-195 | 3 | |
| β-strand | 196-198 | 3 | 20 |
| α-helix | 201-204 | 4 | |
| α-helix | 206-216 | 11 | |
| β-strand | 230-238 | 9 | 18 |
| α-helix | 247-250 | 4 | |
| α-helix | 254-255 | 2 | |
| α-helix | 256-264 | 9 | |
| α-helix | 265-272 | 8 | |
| α-helix | 273-276 | 4 | |
| α-helix | 281-292 | 12 | |
| β-strand | 295 | 1 | 21 |
| α-helix | 296-299 | 4 | |
| α-helix | 300-302 | 3 | |
| β-strand | 303-309 | 7 | 18 |
| α-helix | 316-319 | 4 | |
| β-strand | 337-343 | 7 | 18 |
| β-strand | 344 | 1 | 21 |
| α-helix | 352 | 1 | |
| β-strand | 353-359 | 7 | 18 |
| β-strand | 366-373 | 8 | 18 |
| α-helix | 374-376 | 3 | |
| β-strand | 389-395 | 7 | 18 |
| β-strand | 399-407 | 9 | 18 |
| β-strand | 415-423 | 9 | 18 |
| α-helix | 424-427 | 4 | |
| α-helix | 432-435 | 4 | |
| α-helix | 436-446 | 11 | |
| α-helix | 449-451 | 3 | |
| β-strand | 453 | 1 | 20 |
| α-helix | 455-475 | 21 | |
| α-helix | 477-479 | 3 | |
| β-strand | 480-483 | 4 | 18 |
| α-helix | 490-499 | 10 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Glucose-6-phosphate 1-dehydrogenase | A, B, C, D, E, F, G, H | protein | 514 | HOMO SAPIENS | P11413 (AlphaFold model) |
Sequence of entity 1 (A, B, C, D, E, F, G, H), FASTA
>1QKI_1 GLUCOSE-6-PHOSPHATE 1-DEHYDROGENASE (chains A, B, C, D, E, F, G, H)
AEQVALSRTHVCGILREELFQGDAFHQSDTHIFIIMGASGDLAKKKIYPTIWWLFRDGLL
PENTFIVGYARSRLTVADIRKQSEPFFKATPEEKLKLEDFFARNSYVAGQYDDAASYQRL
NSHMNALHLGSQANRLFYLALPPTVYEAVTKNIHESCMSQIGWNRIIVEKPFGRDLQSSD
RLSNHISSLFREDQIYRIDHYLGKEMVQNLMVLRFANRIFGPIWNRDNIACVILTFKEPF
GTEGRGGYFDEFGIIRDVMQNHLLQMLCLVAMEKPASTNSDDVRDEKVKVLKCISEVQAN
NVVLGQYVGNPDGEGEATKGYLDDPTVPRGSTTATFAAVVLYVENERWDGVPFILRCGKA
LNERKAEVRLQFHDVAGDIFHQQCKRNELVIRVQPNEAVYTKMMTKKPGMFFNPEESELD
LTYGNRYKNVKLPDAYERLILDVFCGSQMHFVRSDELLEAWRIFTPLLHQIELEKPKPIP
YIYGSRGPTEADELMKRVGFQYEGTYKWVNPHKL
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| GOA | Glycolic acid | C2 H4 O3 | 8 |
| NAP | NADP nicotinamide-adenine-dinucleotide phosphate | C21 H28 N7 O17 P3 | 8 |
Water and common crystallization additives (GOL) are not listed.
Primary citation
Human Glucose-6-Phosphate Dehydrogenase: The Crystal Structure Reveals a Structural Nadp+ Molecule and Provides Insights Into Enzyme Deficiency. Au, S.W.N., Gover, S., Lam, V.M.S. et al. Structure (2000) 8:293. DOI 10.1016/S0969-2126(00)00104-0 · PubMed
Other PDB entries of the same protein (UniProt P11413 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 6JYU 1.89 Å, Crystal structure of Human G6PD Canton
- 6E08 1.9 Å, Crystal structure of G6PD in complex with structural NADP
- 7SNH 2.2 Å, Structure of G6PD-D200N tetramer bound to NADP+
- 7ZVE 2.28 Å, K403 acetylated glucose-6-phosphate dehydrogenase (G6PD)
- 7ZVD 2.46 Å, K89 acetylated glucose-6-phosphate dehydrogenase (G6PD) in a complex with structural NADP+
- 2BH9 2.5 Å, X-ray structure of a deletion variant of human glucose 6-phosphate dehydrogenase…
- 7SNI 2.5 Å, Structure of G6PD-D200N tetramer bound to NADP+ and G6P
- 7UC2 2.5 Å, Structure of G6PD-D200N tetramer bound to NADP+ with no symmetry applied
- 6E07 2.6 Å, Crystal structure of Canton G6PD in complex with structural NADP
- 5UKW 2.65 Å, Crystal structure of human Glucose 6-phosphate Dehydrogenase mutant (A277C) complexed…
- 7SNG 2.8 Å, structure of G6PD-WT tetramer
- 2BHL 2.9 Å, X-ray structure of human glucose-6-phosphate dehydrogenase (deletion variant) complexed…
Browse structure collections
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