5UN8: Human O-GlcNAcase
Crystal Structure of human O-GlcNAcase in complex with glycopeptide p53. Determined by X-ray diffraction at 2.13 Å resolution. Released 15 Mar 2017.
- Method
- X-ray diffraction
- Resolution
- 2.13 Å
- Organism
- Homo sapiens
- Chains
- 8
- Atoms
- 15,552
- Mol. weight
- 236.96 kDa
- Ligands
- NAG
- Released
- 15 Mar 2017
Explore 5UN8 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5UN8 contains 95 α-helices and 44 β-strands across 6 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: 23 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 61-66 | 6 | 1 |
| α-helix | 72-74 | 3 | |
| α-helix | 75-87 | 13 | |
| β-strand | 92-95 | 4 | 1 |
| α-helix | 101-103 | 3 | |
| α-helix | 110-112 | 3 | |
| α-helix | 113-128 | 16 | |
| β-strand | 132-137 | 6 | 1 |
| α-helix | 148-162 | 15 | |
| β-strand | 168-172 | 5 | 1 |
| α-helix | 182-187 | 6 | |
| α-helix | 191-205 | 15 | |
| β-strand | 212-215 | 4 | 1 |
| α-helix | 221-223 | 3 | |
| α-helix | 232-240 | 9 | |
| β-strand | 246-249 | 4 | 1 |
| α-helix | 261-271 | 11 | |
| α-helix | 274-275 | 2 | |
| β-strand | 276-279 | 4 | 1 |
| α-helix | 301-306 | 6 | |
| β-strand | 309-312 | 4 | 1 |
| α-helix | 318-321 | 4 | |
| α-helix | 322-332 | 11 | |
| α-helix | 376-388 | 13 | |
| α-helix | 392-395 | 4 | |
| α-helix | 555-564 | 10 | |
| β-strand | 567 | 1 | 2 |
| β-strand | 570 | 1 | 2 |
| α-helix | 573-587 | 15 | |
| α-helix | 589-591 | 3 | |
| α-helix | 605-628 | 24 | |
| α-helix | 634-661 | 28 | |
| α-helix | 684-692 | 9 | |
Chain B: 24 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 61-66 | 6 | 3 |
| α-helix | 72-73 | 2 | |
| α-helix | 75-87 | 13 | |
| β-strand | 92-95 | 4 | 3 |
| α-helix | 101-103 | 3 | |
| α-helix | 110-111 | 2 | |
| α-helix | 113-128 | 16 | |
| β-strand | 132-137 | 6 | 3 |
| α-helix | 148-163 | 16 | |
| β-strand | 168-172 | 5 | 3 |
| α-helix | 179-181 | 3 | |
| α-helix | 182-187 | 6 | |
| α-helix | 191-205 | 15 | |
| β-strand | 212-215 | 4 | 3 |
| α-helix | 221-223 | 3 | |
| α-helix | 232-240 | 9 | |
| β-strand | 246-249 | 4 | 3 |
| α-helix | 261-271 | 11 | |
| α-helix | 274-275 | 2 | |
| β-strand | 276-279 | 4 | 3 |
| α-helix | 301-306 | 6 | |
| β-strand | 309-312 | 4 | 3 |
| α-helix | 318-321 | 4 | |
| α-helix | 322-332 | 11 | |
| α-helix | 376-388 | 13 | |
| α-helix | 392-395 | 4 | |
| α-helix | 555-564 | 10 | |
| β-strand | 567 | 1 | 4 |
| β-strand | 570 | 1 | 4 |
| α-helix | 573-587 | 15 | |
| α-helix | 589-591 | 3 | |
| α-helix | 604-628 | 25 | |
| α-helix | 634-661 | 28 | |
| α-helix | 684-692 | 9 | |
Chain C: 24 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 61-66 | 6 | 5 |
| α-helix | 72-73 | 2 | |
| α-helix | 75-87 | 13 | |
| β-strand | 92-95 | 4 | 5 |
| α-helix | 109-112 | 4 | |
| α-helix | 113-128 | 16 | |
| β-strand | 132-137 | 6 | 5 |
| α-helix | 148-162 | 15 | |
| β-strand | 168-172 | 5 | 5 |
| α-helix | 182-187 | 6 | |
| α-helix | 191-205 | 15 | |
| β-strand | 212-215 | 4 | 5 |
| α-helix | 221-223 | 3 | |
| α-helix | 232-240 | 9 | |
| β-strand | 246-249 | 4 | 5 |
| α-helix | 261-271 | 11 | |
| α-helix | 274-275 | 2 | |
| β-strand | 276-279 | 4 | 5 |
| α-helix | 295-296 | 2 | |
| α-helix | 301-306 | 6 | |
| β-strand | 309-312 | 4 | 5 |
| α-helix | 318-321 | 4 | |
| α-helix | 322-333 | 12 | |
| α-helix | 376-388 | 13 | |
| α-helix | 555-564 | 10 | |
| β-strand | 567 | 1 | 6 |
| β-strand | 570 | 1 | 6 |
| α-helix | 573-587 | 15 | |
| α-helix | 589-591 | 3 | |
| α-helix | 605-629 | 25 | |
| α-helix | 634-662 | 29 | |
| α-helix | 663-665 | 3 | |
| α-helix | 678-680 | 3 | |
| α-helix | 684-691 | 8 | |
Chain D: 23 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 61-66 | 6 | 7 |
| α-helix | 72-74 | 3 | |
| α-helix | 75-87 | 13 | |
| β-strand | 92-95 | 4 | 7 |
| α-helix | 109-112 | 4 | |
| α-helix | 113-128 | 16 | |
| β-strand | 132-137 | 6 | 7 |
| α-helix | 148-163 | 16 | |
| β-strand | 168-172 | 5 | 7 |
| α-helix | 182-185 | 4 | |
| α-helix | 191-205 | 15 | |
| β-strand | 212-215 | 4 | 7 |
| α-helix | 221-223 | 3 | |
| α-helix | 232-240 | 9 | |
| β-strand | 246-249 | 4 | 7 |
| α-helix | 261-271 | 11 | |
| α-helix | 274-275 | 2 | |
| β-strand | 276-279 | 4 | 7 |
| α-helix | 301-306 | 6 | |
| β-strand | 309-312 | 4 | 7 |
| α-helix | 318-321 | 4 | |
| α-helix | 322-334 | 13 | |
| α-helix | 376-388 | 13 | |
| α-helix | 555-564 | 10 | |
| β-strand | 567 | 1 | 8 |
| β-strand | 570 | 1 | 8 |
| α-helix | 573-587 | 15 | |
| α-helix | 589-591 | 3 | |
| α-helix | 605-629 | 25 | |
| α-helix | 634-662 | 29 | |
| α-helix | 663-665 | 3 | |
| α-helix | 678-680 | 3 | |
| α-helix | 684-691 | 8 | |
Chain G: 1 helix, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 147 | 1 | 9 |
| β-strand | 150 | 1 | 9 |
| α-helix | 151-153 | 3 | |
Chain H: 0 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 147 | 1 | 10 |
| β-strand | 150 | 1 | 10 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Protein O-GlcNAcase | A, B, C, D | protein | 504 | Homo sapiens | O60502 (AlphaFold model) |
| P53 peptide | E, F, G, H | protein | 11 | Homo sapiens | P04637 (AlphaFold model) |
Sequence of entity 1 (A, B, C, D), FASTA
>5UN8_1 Protein O-GlcNAcase (chains A, B, C, D)
HFLCGVVEGFYGRPWVMEQRKELFRRLQKWELNTYLYAPKDDYKHRMFWREMYSVEEAEQ
LMTLISAAREYEIEFIYAISPGLDITFSNPKEVSTLKRKLDQVSQFGCRSFALLFDNIDH
NMCAADKEVFSSFAHAQVSITNEIYQYLGEPETFLFCPTEYCGTFCYPNVSQSPYLRTVG
EKLLPGIEVLWTGPKVVSKEIPVESIEEVSKIIKRAPVIWDNIHANDYDQKRLFLGPYKG
RSTELIPRLKGVLTNPNCEFEANYVAIHTLATWYKSNMNGVRKDVVMTDSEDSTVSIQIK
LENEGSDEDIETDVLYSPQMALKLALTEWLQEFGVPHQYSSRGGGGSGGGGSVTLEDLQL
LADLFYLPYEHGPKGAQMLREFQWLRANSSVVSVNCKGKDSEKIEEWRSRAAKFEEMCGL
VMGMFTRLSNCANRTILYDMYSYVWDIKSIMSMVKSFVQWLGCRSHSSAQFLIGDQEPWA
FRGGLAGEFQRLLPIDGANDLFFQ
Sequence of entity 2 (E, F, G, H), FASTA
>5UN8_2 P53 peptide (chains E, F, G, H)
QLWVDSTPPPG
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 4 |
Primary citation
Structures of human O-GlcNAcase and its complexes reveal a new substrate recognition mode. Li, B., Li, H., Lu, L. et al. Nat Struct Mol Biol (2017) 24:362-369. DOI 10.1038/nsmb.3390 · PubMed
Other PDB entries of the same protein (UniProt O60502 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 5M7U 2.3 Å, Structure of human O-GlcNAc hydrolase with new iminocyclitol type inhibitor
- 11LJ 2.33 Å, Human oga in complex with ligand 24
- 5M7R 2.35 Å, Structure of human O-GlcNAc hydrolase
- 5M7S 2.4 Å, Structure of human O-GlcNAc hydrolase with bound transition state analog ThiametG
- 7OU6 2.41 Å, Human O-GlcNAc hydrolase in complex with DNJNAc-thiazolidines
- 5TKE 2.48 Å, Crystal Structure of Eukaryotic Hydrolase
- 5UN9 2.5 Å, The crystal structure of human O-GlcNAcase in complex with Thiamet-G
- 8P0L 2.5 Å, Crystal structure of human O-GlcNAcase in complex with an S-linked CKII peptide
- 9BA8 2.54 Å, O-GlcNAcase (OGA) inhibitor complex for the Treatment of Alzheimer's Disease
- 2YDQ 2.6 Å, CpOGA D298N in complex with hOGA-derived O-GlcNAc peptide
- 5M7T 2.6 Å, Structure of human O-GlcNAc hydrolase with PugNAc type inhibitor
- 5VVO 2.6 Å, Structural Investigations of the Substrate Specificity of Human O-GlcNAcase
Browse structure collections
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