MolNFT v1 · #82321 · protein
Crystal structure of the carboxy-terminal ribonuclease domain of colicin E5 R33Q mutant
3VJ7 · Colicin-E5: “Crystal structure of the carboxy-terminal ribonuclease domain of colicin E5 R33Q mutant”. X-ray diffraction, 2 ligands (3PD, UM3), 1 pocket (best druggability 0.37). MolNFT v1 #82321 on GenesisL1: 3D structure, binding…
- PDB
- 3VJ7
- Type
- protein
- Length
- 94 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Colicin-E5
- EC
- 3.1.-.-
- UniProt
- P18000
- Ligands
- 3PD, UM3
- Pockets
- 1 · best druggability 0.37
Structure
x-ray diffraction · 1 distinct chain · 23% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Colicin-E5 (EC 3.1.-.-) | protein | 94 | 23% helix, 31% strand | P18000 |
Ligands and binding sites
- 3PD · 2-amino-9-(2-deoxy-3-O-phosphonopentofuranosyl)-1,9-dihydro-6H-purin-6-one · ligand · chains A
- UM3 · 2'-deoxyuridine 3'-monophosphate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.37 | 0.79 | 19 | UM3 |
Compared structures
- 3VJ7 · Crystal structure of the carboxy-terminal ribonuclease domain of Colicin E5 R33Q mutant · the same entry in another collection · chain A against A, TM-score 1.00
- P18000 · AlphaFold monomer V2.0 prediction for colicin-E5 (P18000) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 P18000
- Elsewhere: RCSB PDB 3VJ7 · PDBe 3VJ7 · UniProt P18000
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