Structure of GGCX-BGP-menaquinone-4 epoxide complex. Determined by electron microscopy at 3.06 Å resolution. Released 29 Jan 2025.
Explore 9BUX in 3D Show helices and sheets RCSB PDB PDBe
9BUX contains 38 α-helices and 20 β-strands across 2 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.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 35-38 | 4 | |
| α-helix | 42-45 | 4 | |
| α-helix | 49-55 | 7 | |
| β-strand | 59 | 1 | 1 |
| α-helix | 62-76 | 15 | |
| α-helix | 78-81 | 4 | |
| α-helix | 108-111 | 4 | |
| α-helix | 112-131 | 20 | |
| α-helix | 135-151 | 17 | |
| α-helix | 154-156 | 3 | |
| α-helix | 159-173 | 15 | |
| α-helix | 183-186 | 4 | |
| β-strand | 193 | 1 | 2 |
| β-strand | 195 | 1 | 1 |
| α-helix | 198-217 | 20 | |
| α-helix | 221-224 | 4 | |
| α-helix | 232-234 | 3 | |
| α-helix | 236-238 | 3 | |
| α-helix | 241-243 | 3 | |
| α-helix | 247-249 | 3 | |
| α-helix | 250-257 | 8 | |
| α-helix | 260-264 | 5 | |
| α-helix | 276-293 | 18 | |
| α-helix | 299-305 | 7 | |
| α-helix | 307-309 | 3 | |
| α-helix | 315-320 | 6 | |
| α-helix | 336-337 | 2 | |
| β-strand | 338 | 1 | 2 |
| α-helix | 339 | 1 | |
| α-helix | 358-373 | 16 | |
| α-helix | 377-379 | 3 | |
| β-strand | 406-416 | 11 | 3 |
| β-strand | 423-426 | 4 | 3 |
| α-helix | 441-454 | 14 | |
| α-helix | 455-458 | 4 | |
| β-strand | 466-473 | 8 | 3 |
| β-strand | 478 | 1 | 4 |
| β-strand | 479-480 | 2 | 3 |
| β-strand | 482 | 1 | 5 |
| β-strand | 502 | 1 | 5 |
| α-helix | 503-505 | 3 | |
| α-helix | 507-509 | 3 | |
| α-helix | 513-521 | 9 | |
| β-strand | 527-534 | 8 | 4 |
| β-strand | 539-543 | 5 | 6 |
| β-strand | 551-557 | 7 | 4 |
| β-strand | 560-564 | 5 | 6 |
| β-strand | 569-572 | 4 | 6 |
| β-strand | 578-581 | 4 | 4 |
| β-strand | 586-591 | 6 | 6 |
| α-helix | 596 | 1 | |
| β-strand | 597-604 | 8 | 4 |
| α-helix | 606-622 | 17 | |
| α-helix | 655-673 | 19 | |
| α-helix | 677-707 | 31 | |
| α-helix | 713-723 | 11 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 36-37 | 2 | 3 |
| α-helix | 89-95 | 7 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Vitamin K-dependent gamma-carboxylase | A | protein | 766 | Homo sapiens | P38435 (AlphaFold model) |
| Osteocalcin | B | protein | 106 | Homo sapiens | P02818 (AlphaFold model) |
>9BUX_1 Vitamin K-dependent gamma-carboxylase (chains A) MAVSAGSARTSPSSDKVQKDKAELISGPRQDSRIGKLLGFEWTDLSSWRRLVTLLNRPTD PASLAVFRFLFGFLMVLDIPQERGLSSLDRKYLDGLDVCRFPLLDALRPLPLDWMYLVYT IMFLGALGMMLGLCYRISCVLFLLPYWYVFLLDKTSWNNHSYLYGLLAFQLTFMDANHYW SVDGLLNAHRRNAHVPLWNYAVLRGQIFIVYFIAGVKKLDADWVEGYSMEYLSRHWLFSP FKLLLSEELTSLLVVHWGGLLLDLSAGFLLFFDVSRSIGLFFVSYFHCMNSQLFSIGMFS YVMLASSPLFCSPEWPRKLVSYCPRRLQQLLPLKAAPQPSVSCVYKRSRGKSGQKPGLRH QLGAAFTLLYLLEQLFLPYSHFLTQGYNNWTNGLYGYSWDMMVHSRSHQHVKITYRDGRT GELGYLNPGVFTQSRRWKDHADMLKQYATCLSRLLPKYNVTEPQIYFDIWVSINDRFQQR IFDPRVDIVQAAWSPFQRTSWVQPLLMDLSPWRAKLQEIKSSLDNHTEVVFIADFPGLHL ENFVSEDLGNTSIQLLQGEVTVELVAEQKNQTLREGEKMQLPAGEYHKVYTTSPSPSCYM YVYVNTTELALEQDLAYLQELKEKVENGSETGPLPPELQPLLEGEVKGGPEPTPLVQTFL RRQQRLQEIERRRNTPFHERFFRFLLRKLYVFRRSFLMTCISLRNLILGRPSLEQLAQEV TYANLRPFEAVGELNPSNTDSSHSNPPESNPDPVHSEFDYKDDDDK
>9BUX_2 Osteocalcin (chains B) MRALTLLALLALAALCIAGQAGAKPSGAESSKGAAFVSKQEGSEVVKRPRRYLYQWLGAP VPYPDPLEPRREVCELNPDCDELADHIGFQEAYRRFYGPVHHHHHH
| ID | Name | Formula | Copies |
|---|---|---|---|
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 2 |
| CLR | Cholesterol | C27 H46 O | 1 |
| POV | (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl… | C42 H82 N O8 P | 1 |
| A1AT1 | (1aR,7aS)-1a-methyl-7a-[(2E,6E,10E)-3,7,11,15-tetramethylhexadeca-2,6,10,14-tet… | C31 H40 O3 | 1 |
Structure and mechanism of vitamin-K-dependent gamma-glutamyl carboxylase. Wang, R., Chen, B., Elghobashi-Meinhardt, N. et al. Nature (2025) 639:808-815. DOI 10.1038/s41586-024-08484-9 · PubMed
Other PDB entries of the same protein (UniProt P38435 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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