MolNFT v1 · #118216 · protein
Crystal structure of the native, di-zinc metallo-beta-lactamase imp-1
5EV6: “Crystal structure of the native, di-zinc metallo-beta-lactamase imp-1”. X-ray diffraction, 1 ligand (ZN), 9 pockets (best druggability 0.78). MolNFT v1 #118216 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5EV6
- Type
- protein
- Length
- 882 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase imp-1
- EC
- 3.5.2.6
- UniProt
- P52699
- Ligands
- ZN
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase imp-1 (EC 3.5.2.6) | protein | 219 | 27% helix, 32% strand | P52699 |
| B | Beta-lactamase imp-1 (EC 3.5.2.6) | protein | 223 | 26% helix, 30% strand | P52699 |
| C | Beta-lactamase imp-1 (EC 3.5.2.6) | protein | 222 | 27% helix, 31% strand | P52699 |
| D | Beta-lactamase imp-1 (EC 3.5.2.6) | protein | 218 | 27% helix, 32% strand | P52699 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 344 | 0.78 | 0.88 | 58 | ZN |
| 2 | 342 | 0.72 | 0.84 | 37 | ZN |
| 3 | 363 | 0.71 | 0.83 | 45 | empty |
| 4 | 161 | 0.49 | 0.78 | 24 | empty |
| 5 | 51 | 0.44 | 0.84 | 12 | empty |
Interfaces
4 interfaces between chains.
- A–D · 718 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 463 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 462 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 42 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5EV6 · Crystal structure of the native, di-zinc metallo-beta-lactamase IMP-1 · the same entry in another collection · chain D against D, TM-score 1.00
- P52699 · AlphaFold monomer V2.0 prediction for metallo-beta-lactamase type 2 (P52699) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 P52699
- Elsewhere: RCSB PDB 5EV6 · PDBe 5EV6 · UniProt P52699
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