Vitamin K-dependent gamma-carboxylase with protein C propeptide and glutamate-rich region and with vitamin K hydroquinone. Determined by electron microscopy at 3.4 Å resolution. Released 22 Jan 2025.
Explore 9BVM in 3D Show helices and sheets RCSB PDB PDBe
9BVM contains 44 α-helices and 22 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 | 33-38 | 6 | |
| α-helix | 42-45 | 4 | |
| α-helix | 48-55 | 8 | |
| β-strand | 59 | 1 | 1 |
| α-helix | 62-78 | 17 | |
| α-helix | 79-83 | 5 | |
| α-helix | 88-90 | 3 | |
| α-helix | 109-111 | 3 | |
| α-helix | 112-131 | 20 | |
| α-helix | 135-152 | 18 | |
| α-helix | 159-171 | 13 | |
| α-helix | 182-186 | 5 | |
| α-helix | 188-190 | 3 | |
| 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 | 240-243 | 4 | |
| α-helix | 247-249 | 3 | |
| α-helix | 250-257 | 8 | |
| α-helix | 258-269 | 12 | |
| α-helix | 276-293 | 18 | |
| α-helix | 299-306 | 8 | |
| α-helix | 307-310 | 4 | |
| α-helix | 315-321 | 7 | |
| α-helix | 325-328 | 4 | |
| α-helix | 336-337 | 2 | |
| β-strand | 338 | 1 | 2 |
| α-helix | 339 | 1 | |
| α-helix | 359-376 | 18 | |
| α-helix | 377-379 | 3 | |
| α-helix | 385-387 | 3 | |
| β-strand | 406-416 | 11 | 3 |
| β-strand | 423-426 | 4 | 3 |
| α-helix | 436-438 | 3 | |
| α-helix | 441-454 | 14 | |
| α-helix | 455-458 | 4 | |
| β-strand | 464-473 | 10 | 3 |
| β-strand | 478 | 1 | 4 |
| β-strand | 479-480 | 2 | 3 |
| β-strand | 482 | 1 | 5 |
| β-strand | 494 | 1 | 6 |
| β-strand | 497 | 1 | 6 |
| β-strand | 502 | 1 | 5 |
| α-helix | 503-505 | 3 | |
| α-helix | 507-509 | 3 | |
| α-helix | 512-520 | 9 | |
| β-strand | 528-534 | 7 | 4 |
| β-strand | 539-543 | 5 | 7 |
| β-strand | 551-557 | 7 | 4 |
| β-strand | 560-564 | 5 | 7 |
| β-strand | 569-573 | 5 | 7 |
| β-strand | 578-581 | 4 | 4 |
| β-strand | 586-591 | 6 | 7 |
| β-strand | 597-603 | 7 | 4 |
| α-helix | 606-626 | 21 | |
| α-helix | 633-635 | 3 | |
| α-helix | 638-643 | 6 | |
| α-helix | 650-653 | 4 | |
| α-helix | 654-673 | 20 | |
| α-helix | 677-708 | 32 | |
| α-helix | 713-723 | 11 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 27-28 | 2 | 3 |
| α-helix | 30-33 | 4 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Vitamin K-dependent gamma-carboxylase | A | protein | 732 | Homo sapiens | P38435 (AlphaFold model) |
| Activation peptide | P | protein | 70 | Homo sapiens | P04070 (AlphaFold model) |
>9BVM_1 Vitamin K-dependent gamma-carboxylase (chains A) GPRQDSRIGKLLGFEWTDLSSWRRLVTLLNRPTDPASLAVFRFLFGFLMVLDIPQERGLS SLDRKYLDGLDVCRFPLLDALRPLPLDWMYLVYTIMFLGALGMMLGLCYRISCVLFLLPY WYVFLLDKTSWNNHSYLYGLLAFQLTFMDANHYWSVDGLLNAHRRNAHVPLWNYAVLRGQ IFIVYFIAGVKKLDADWVEGYSMEYLSRHWLFSPFKLLLSEELTSLLVVHWGGLLLDLSA GFLLFFDVSRSIGLFFVSYFHCMNSQLFSIGMFSYVMLASSPLFCSPEWPRKLVSYCPRR LQQLLPLKAAPQPSVSCVYKRSRGKSGQKPGLRHQLGAAFTLLYLLEQLFLPYSHFLTQG YNNWTNGLYGYSWDMMVHSRSHQHVKITYRDGRTGELGYLNPGVFTQSRRWKDHADMLKQ YATCLSRLLPKYNVTEPQIYFDIWVSINDRFQQRIFDPRVDIVQAAWSPFQRTSWVQPLL MDLSPWRAKLQEIKSSLDNHTEVVFIADFPGLHLENFVSEDLGNTSIQLLQGEVTVELVA EQKNQTLREGEKMQLPAGEYHKVYTTSPSPSCYMYVYVNTTELALEQDLAYLQELKEKVE NGSETGPLPPELQPLLEGEVKGGPEPTPLVQTFLRRQQRLQEIERRRNTPFHERFFRFLL RKLYVFRRSFLMTCISLRNLILGRPSLEQLAQEVTYANLRPFEAVGELNPSNTDSSHSNP PESNPDPVHSEF
>9BVM_2 Activation peptide (chains P) TPAPLDSVFSSSERAHQVLRIRKRANSFLEELRHSSLERECIEEICDFEEAKEIFQNVDD TLAFWSKHVD
| ID | Name | Formula | Copies |
|---|---|---|---|
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 1 |
| 6PL | (4S,7R)-4-hydroxy-n,n,n-trimethyl-9-oxo-7-[(palmitoyloxy)methyl]-3,5,8-trioxa-4… | C42 H85 N O8 P | 2 |
| A1AVC | vitamin K1 hydroquinone | C31 H48 O2 | 1 |
Molecular basis of vitamin-K-driven gamma-carboxylation at the membrane interface. Cao, Q., Ammerman, A., Saimi, M. et al. Nature (2025) 639:816-824. DOI 10.1038/s41586-025-08648-1 · 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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