MolNFT v1 · #21528 · protein
Crystal structure of bovine factor vai
1SDD · Coagulation factor V: “Crystal structure of bovine factor vai”. X-ray diffraction, 3 ligands (NAG, CA, CU), 10 pockets (best druggability 0.78). MolNFT v1 #21528 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1SDD
- Type
- protein
- Length
- 869 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor V
- UniProt
- Q28107
- Ligands
- NAG, CA, CU
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coagulation factor V | protein | 268 | 6% helix, 28% strand | Q28107 |
| B | Coagulation factor V | protein | 601 | 4% helix, 45% strand | Q28107 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
- CA · Calcium ion · metal · chains A
- CU · Copper (II) ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 946 | 0.78 | 0.80 | 86 | empty |
| 2 | 851 | 0.75 | 0.79 | 91 | empty |
| 3 | 121 | 0.69 | 0.91 | 25 | empty |
| 4 | 195 | 0.57 | 0.80 | 24 | empty |
| 5 | 282 | 0.55 | 0.76 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 1593 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 glycan, 4 disulfide (N-glycosylation, disulfide).
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 Q28107
- Elsewhere: RCSB PDB 1SDD · PDBe 1SDD · UniProt Q28107
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