MolNFT v1 · #162375 · protein
Structure of imp-13 metallo-beta-lactamase complexed with hydrolysed meropenem
6R73: “Structure of imp-13 metallo-beta-lactamase complexed with hydrolysed meropenem”. X-ray diffraction, 2 ligands (LMP, ZN), 3 pockets (best druggability 0.71). MolNFT v1 #162375 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6R73
- Type
- protein
- Length
- 432 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q7WYA8
- Ligands
- LMP, ZN
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-lactamase (EC 3.5.2.6) | protein | 216 | 28% helix, 31% strand | Q7WYA8 |
Ligands and binding sites
- LMP · (2~{S},3~{R},4~{S})-2-[(2~{S},3~{R})-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-4-[(3~{S},5~{S})-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl-3-methyl-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 378 | 0.71 | 0.82 | 50 | empty |
| 2 | 153 | 0.47 | 0.77 | 23 | LMP, ZN |
| 3 | 143 | 0.45 | 0.76 | 21 | LMP, ZN |
Interfaces
1 interface between chains.
- A–B · 712 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6R73 · Structure of IMP-13 metallo-beta-lactamase complexed with hydrolysed meropenem · the same entry in another collection · 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 Q7WYA8
- Elsewhere: RCSB PDB 6R73 · PDBe 6R73 · UniProt Q7WYA8
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