double-mutant (K217A & K218A) Vitamin K-dependent gamma-carboxylase in complex with Coagulation factor IX and vitamin K. Determined by electron microscopy at 2.59 Å resolution. Released 8 Oct 2025.
Explore 9L6R in 3D Show helices and sheets RCSB PDB PDBe
9L6R contains 45 α-helices and 21 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 | 58-59 | 2 | 2 |
| α-helix | 62-78 | 17 | |
| α-helix | 88-91 | 4 | |
| α-helix | 109-111 | 3 | |
| α-helix | 112-131 | 20 | |
| α-helix | 135-152 | 18 | |
| α-helix | 154-156 | 3 | |
| α-helix | 159-171 | 13 | |
| α-helix | 182-186 | 5 | |
| α-helix | 188-190 | 3 | |
| β-strand | 193 | 1 | 3 |
| β-strand | 195-196 | 2 | 2 |
| α-helix | 198-217 | 20 | |
| α-helix | 221-225 | 5 | |
| α-helix | 232-234 | 3 | |
| α-helix | 236-238 | 3 | |
| α-helix | 239-242 | 4 | |
| α-helix | 247-250 | 4 | |
| α-helix | 251-258 | 8 | |
| α-helix | 259-271 | 13 | |
| 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 | 3 |
| α-helix | 339 | 1 | |
| α-helix | 358-376 | 19 | |
| α-helix | 377-379 | 3 | |
| α-helix | 385-387 | 3 | |
| β-strand | 406-416 | 11 | 1 |
| β-strand | 423-426 | 4 | 1 |
| α-helix | 436-438 | 3 | |
| α-helix | 441-454 | 14 | |
| α-helix | 455-458 | 4 | |
| β-strand | 464-473 | 10 | 1 |
| β-strand | 478 | 1 | 4 |
| β-strand | 479-480 | 2 | 1 |
| β-strand | 482 | 1 | 5 |
| β-strand | 502 | 1 | 5 |
| α-helix | 503-505 | 3 | |
| α-helix | 507-512 | 6 | |
| α-helix | 513-521 | 9 | |
| β-strand | 528-534 | 7 | 4 |
| β-strand | 539-543 | 5 | 6 |
| β-strand | 551-557 | 7 | 4 |
| β-strand | 560-564 | 5 | 6 |
| β-strand | 569-573 | 5 | 6 |
| β-strand | 578-581 | 4 | 4 |
| β-strand | 586-591 | 6 | 6 |
| β-strand | 597-603 | 7 | 4 |
| α-helix | 606-626 | 21 | |
| α-helix | 633-635 | 3 | |
| α-helix | 636-638 | 3 | |
| α-helix | 639-643 | 5 | |
| α-helix | 650-653 | 4 | |
| α-helix | 654-673 | 20 | |
| α-helix | 677-707 | 31 | |
| α-helix | 713-723 | 11 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 31 | 1 | 1 |
| α-helix | 34-37 | 4 | |
| β-strand | 50 | 1 | 1 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Coagulation factor IX | C | protein | 461 | Homo sapiens | P00740 (AlphaFold model) |
| Vitamin K-dependent gamma-carboxylase | A | protein | 758 | Homo sapiens | P38435 (AlphaFold model) |
>9L6R_1 Coagulation factor IX (chains C) MQRVNMIMAESPGLITICLLGYLLSAECTVFLDHENANKILNRPKRYNSGKLEEFVQGNL ERECMEEKCSFEEAREVFENTERTTEFWKQYVDGDQCESNPCLNGGSCKDDINSYECWCP FGFEGKNCELDVTCNIKNGRCEQFCKNSADNKVVCSCTEGYRLAENQKSCEPAVPFPCGR VSVSQTSKLTRAETVFPDVDYVNSTEAETILDNITQSTQSFNDFTRVVGGEDAKPGQFPW QVVLNGKVDAFCGGSIVNEKWIVTAAHCVETGVKITVVAGEHNIEETEHTEQKRNVIRII PHHNYNAAINKYNHDIALLELDEPLVLNSYVTPICIADKEYTNIFLKFGSGYVSGWGRVF HKGRSALVLQYLRVPLVDRATCLRSTKFTIYNNMFCAGFHEGGRDSCQGDSGGPHVTEVE GTSFLTGIISWGEECAMKGKYGIYTKVSRYVNWIKEKTKLT
>9L6R_2 Vitamin K-dependent gamma-carboxylase (chains A) MAVSAGSARTSPSSDKVQKDKAELISGPRQDSRIGKLLGFEWTDLSSWRRLVTLLNRPTD PASLAVFRFLFGFLMVLDIPQERGLSSLDRKYLDGLDVCRFPLLDALRPLPLDWMYLVYT IMFLGALGMMLGLCYRISCVLFLLPYWYVFLLDKTSWNNHSYLYGLLAFQLTFMDANHYW SVDGLLNAHRRNAHVPLWNYAVLRGQIFIVYFIAGVAALDADWVEGYSMEYLSRHWLFSP FKLLLSEELTSLLVVHWGGLLLDLSAGFLLFFDVSRSIGLFFVSYFHCMNSQLFSIGMFS YVMLASSPLFCSPEWPRKLVSYCPRRLQQLLPLKAAPQPSVSCVYKRSRGKSGQKPGLRH QLGAAFTLLYLLEQLFLPYSHFLTQGYNNWTNGLYGYSWDMMVHSRSHQHVKITYRDGRT GELGYLNPGVFTQSRRWKDHADMLKQYATCLSRLLPKYNVTEPQIYFDIWVSINDRFQQR IFDPRVDIVQAAWSPFQRTSWVQPLLMDLSPWRAKLQEIKSSLDNHTEVVFIADFPGLHL ENFVSEDLGNTSIQLLQGEVTVELVAEQKNQTLREGEKMQLPAGEYHKVYTTSPSPSCYM YVYVNTTELALEQDLAYLQELKEKVENGSETGPLPPELQPLLEGEVKGGPEPTPLVQTFL RRQQRLQEIERRRNTPFHERFFRFLLRKLYVFRRSFLMTCISLRNLILGRPSLEQLAQEV TYANLRPFEAVGELNPSNTDSSHSNPPESNPDPVHSEF
| ID | Name | Formula | Copies |
|---|---|---|---|
| CLR | Cholesterol | C27 H46 O | 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 |
| A1EMC | 2-methyl-3-[(2~{E},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetrae… | C31 H42 O2 | 1 |
Molecular basis of vitamin K-dependent protein gamma-glutamyl carboxylation. Zhong, Q., Chen, D., Xu, J. et al. Cell Res (2025) 35:917-920. DOI 10.1038/s41422-025-01185-6 · PubMed
Other PDB entries of the same protein (UniProt P00740 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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