MolNFT v1 · #156412 · protein
Hapc-C25K23 Fab complex
6M3B · Vitamin K-dependent protein C heavy chain: “Hapc-C25K23 Fab complex”. X-ray diffraction, 1 ligand (NAG), 9 pockets (best druggability 0.58). MolNFT v1 #156412 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6M3B
- Type
- protein
- Length
- 756 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitamin K-dependent protein C heavy chain; Vitamin K-dependent protein C light chain…
- EC
- 3.4.21.69
- UniProt
- P04070
- Ligands
- NAG
- Pockets
- 9 · best druggability 0.58
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitamin K-dependent protein C heavy chain (EC 3.4.21.69) | protein | 228 | 14% helix, 37% strand | P04070 |
| D | Vitamin K-dependent protein C light chain (EC 3.4.21.69) | protein | 91 | 4% helix, 26% strand | P04070 |
| B | C25K23 Fab L chain | protein | 214 | 7% helix, 50% strand | — |
| C | C25K23 Fab H chain | protein | 223 | 7% helix, 46% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 273 | 0.58 | 0.78 | 40 | empty |
| 2 | 294 | 0.53 | 0.75 | 47 | empty |
| 3 | 282 | 0.52 | 0.75 | 37 | empty |
| 4 | 50 | 0.41 | 0.82 | 14 | empty |
| 5 | 107 | 0.41 | 0.76 | 22 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1860 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 816 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 814 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 93 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 15 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P04070
- Elsewhere: RCSB PDB 6M3B · PDBe 6M3B · UniProt P04070
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