Research workbench
Crystal structure of RUSSELL'S viper venom metalloproteinase
Analyse Crystal structure of RUSSELL'S viper venom metalloproteinase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2E3X
- Type
- protein
- Length
- 665 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor X-activating enzyme heavy chain; Coagulation factor X-activating…
- EC
- 3.4.24.58
- UniProt
- Q7LZ61, Q4PRD2, Q4PRD1
- Ligands
- GM6, NAG, MAN, CA, ZN
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coagulation factor X-activating enzyme heavy chain (EC 3.4.24.58) | protein | 416 | 23% helix, 18% strand | Q7LZ61 |
| B | Coagulation factor X-activating enzyme light chain 2 | protein | 129 | 20% helix, 30% strand | Q4PRD2 |
| C | Coagulation factor X-activating enzyme light chain 1 | protein | 120 | 21% helix, 29% strand | Q4PRD1 |
Ligands and binding sites
- GM6 · 3-(N-hydroxycarboxamido)-2-isobutylpropanoyl-trp-methylamide · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, C, B
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- CA · Calcium ion · metal · 5 copies · chains A, B
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1170 | 0.78 | 0.80 | 110 | CA |
| 2 | 254 | 0.63 | 0.81 | 25 | empty |
| 3 | 280 | 0.55 | 0.76 | 51 | empty |
| 4 | 186 | 0.49 | 0.76 | 37 | ZN, GM6 |
| 5 | 106 | 0.34 | 0.73 | 15 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1969 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 515 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 195 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 2E3X · Crystal structure of Russell's viper venom metalloproteinase · the same entry in another collection · chain A against A, TM-score 1.00
- Q4PRD1 · AlphaFold monomer V2.0 prediction for snaclec coagulation factor X-activating enzyme… · a predicted model of the same protein · chain C against A, TM-score 0.93
- Q7LZ61 · AlphaFold monomer V2.0 prediction for coagulation factor X-activating enzyme heavy chain… · a predicted model of the same protein · chain A against A, TM-score 0.92
- Q4PRD2 · AlphaFold monomer V2.0 prediction for snaclec coagulation factor X-activating enzyme… · a predicted model of the same protein · chain B against A, TM-score 0.79
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 Q7LZ61
- Every structure of UniProt Q4PRD2
- Every structure of UniProt Q4PRD1
- Elsewhere: RCSB PDB 2E3X · PDBe 2E3X · UniProt Q7LZ61 · UniProt Q4PRD2 · UniProt Q4PRD1
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