MolNFT v1 · #66494 · protein
Cobra venom factor (cvf) in complex with human factor B
3HRZ: “Cobra venom factor (cvf) in complex with human factor B”. X-ray diffraction, 4 ligands (NAG, MG, K), 20 pockets (best druggability 0.85). MolNFT v1 #66494 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3HRZ
- Type
- protein
- Length
- 1,902 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cobra venom factor; Complement factor B
- EC
- 3.4.21.47
- UniProt
- Q91132, P00751
- Ligands
- NAG, MG, K, PO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cobra venom factor | protein | 614 | 10% helix, 50% strand | Q91132 |
| B | Cobra venom factor | protein | 233 | 3% helix, 54% strand | Q91132 |
| C | Cobra venom factor | protein | 362 | 15% helix, 45% strand | Q91132 |
| D | Complement factor B (EC 3.4.21.47) | protein | 693 | 21% helix, 29% strand | P00751 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains D, A, C
- MG · Magnesium ion · metal · 2 copies · chains A, C, D
- K · Potassium ion · metal · chains A, C
- PO4 · Phosphate ion · ion · 5 copies · chains B, C, D
- P6G · Hexaethylene glycol · additive · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 681 | 0.85 | 0.89 | 64 | empty |
| 2 | 1198 | 0.85 | 0.86 | 116 | PO4 |
| 3 | 738 | 0.75 | 0.80 | 55 | P6G |
| 4 | 530 | 0.70 | 0.80 | 70 | empty |
| 5 | 510 | 0.70 | 0.80 | 50 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3645 Ų buried · 54 hydrogen bonds · protein-protein
- B–C · 3496 Ų buried · 72 hydrogen bonds · protein-protein
- C–D · 1216 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 1209 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 978 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 3HRZ · Cobra Venom Factor (CVF) in complex with human factor B · the same entry in another collection · chain D against D, TM-score 1.00
- Q91132 · AlphaFold monomer V2.0 prediction for cobra venom factor (Q91132) · a predicted model of the same protein · chain A against A, TM-score 0.95
- P00751 · AlphaFold monomer V2.0 prediction for complement factor B (P00751) · a predicted model of the same protein · chain D against A, TM-score 0.64
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 Q91132
- Every structure of UniProt P00751
- Elsewhere: RCSB PDB 3HRZ · PDBe 3HRZ · UniProt Q91132 · UniProt P00751
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