Research workbench
Cobra venom factor (cvf) in complex with human factor B
Analyse Cobra venom factor (cvf) in complex with human factor B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HS0
- Type
- protein
- Length
- 3,824 residues
- Chains
- 8
- 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
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 7 distinct chains · 14% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cobra venom factor | protein | 613 | 9% helix, 49% strand | Q91132 |
| B, G | Cobra venom factor | protein | 233 | 3% helix, 53% strand | Q91132 |
| C | Cobra venom factor | protein | 359 | 11% helix, 44% strand | Q91132 |
| D | Complement factor B (EC 3.4.21.47) | protein | 699 | 21% helix, 26% strand | P00751 |
| F | Cobra venom factor | protein | 617 | 8% helix, 48% strand | Q91132 |
| H | Cobra venom factor | protein | 366 | 14% helix, 45% strand | Q91132 |
| I | Complement factor B (EC 3.4.21.47) | protein | 704 | 21% helix, 26% strand | P00751 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains D, I, A, C, F, H
- MG · Magnesium ion · metal · 4 copies · chains A, C, D, F, H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 869 | 0.86 | 0.88 | 78 | empty |
| 2 | 820 | 0.86 | 0.88 | 78 | empty |
| 3 | 565 | 0.79 | 0.85 | 63 | empty |
| 4 | 579 | 0.78 | 0.84 | 53 | empty |
| 5 | 694 | 0.76 | 0.82 | 52 | empty |
Interfaces
18 interfaces between chains.
- F–G · 3729 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 3719 Ų buried · 56 hydrogen bonds · protein-protein
- G–H · 3561 Ų buried · 72 hydrogen bonds · protein-protein
- B–C · 3463 Ų buried · 70 hydrogen bonds · protein-protein
- H–I · 1105 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 3HS0 · Cobra Venom Factor (CVF) in complex with human factor B · the same entry in another collection · chain I against I, TM-score 1.00
- Q91132 · AlphaFold monomer V2.0 prediction for cobra venom factor (Q91132) · a predicted model of the same protein · chain F against A, TM-score 0.96
- P00751 · AlphaFold monomer V2.0 prediction for complement factor B (P00751) · a predicted model of the same protein · chain I against A, TM-score 0.61
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 3HS0 · PDBe 3HS0 · UniProt Q91132 · UniProt P00751
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