Research workbench
Crystal structure of metallo-beta-lactamase imp-1 in complex with citrate.
Analyse Crystal structure of metallo-beta-lactamase imp-1 in complex with citrate. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DTM
- 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
- ZN
- Pockets
- 7 · best druggability 0.79
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
- 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
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 | 971 | 0.79 | 0.81 | 84 | ZN, FLC |
| 2 | 873 | 0.78 | 0.81 | 77 | ZN, FLC |
| 3 | 305 | 0.63 | 0.80 | 40 | empty |
| 4 | 100 | 0.47 | 0.80 | 16 | ZN, FLC |
| 5 | 56 | 0.44 | 0.83 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–D · 676 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 634 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7DTM · Crystal structure of metallo-beta-lactamase IMP-1 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 C 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 7DTM · PDBe 7DTM · UniProt P52699
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.