MolNFT v1 · #176653 · protein
Crystal structure of metallo-beta-lactamase imp-1 mutant (D120E) in complex with citrate.
7DTN · Metallo-beta-lactamase type 2: “Crystal structure of metallo-beta-lactamase imp-1 mutant (D120E) in complex with citrate.”. X-ray diffraction, 2 ligands (AE3, ZN), 9 pockets (best druggability 0.78). MolNFT v1 #176653 on GenesisL1…
- PDB
- 7DTN
- Type
- protein
- Length
- 872 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metallo-beta-lactamase type 2
- EC
- 3.5.2.6
- UniProt
- P52699
- Ligands
- AE3, ZN
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Metallo-beta-lactamase type 2 (EC 3.5.2.6) | protein | 218 | 27% helix, 32% strand | P52699 |
Ligands and binding sites
- AE3 · 2-(2-ethoxyethoxy)ethanol · ligand · 4 copies · chains A, C, B, D
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- FLC · Citrate anion · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 773 | 0.78 | 0.82 | 64 | ZN, FLC, AE3 |
| 2 | 767 | 0.77 | 0.81 | 58 | FLC, AE3, ZN |
| 3 | 319 | 0.66 | 0.81 | 45 | empty |
| 4 | 328 | 0.62 | 0.78 | 40 | empty |
| 5 | 217 | 0.58 | 0.80 | 25 | empty |
Interfaces
4 interfaces between chains.
- B–D · 697 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 685 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 490 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 227 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 7DTN · Crystal structure of metallo-beta-lactamase IMP-1 mutant (D120E) in complex with citrate. · 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 0.99
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 7DTN · PDBe 7DTN · UniProt P52699
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