Research workbench
Structure of imp-13 metallo-beta-lactamase complexed with hydrolysed imipenem
Analyse Structure of imp-13 metallo-beta-lactamase complexed with hydrolysed imipenem in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RZR
- Type
- protein
- Length
- 436 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
- 8YF, ZN
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 219 | 28% helix, 31% strand | Q7WYA8 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 217 | 27% helix, 31% strand | Q7WYA8 |
Ligands and binding sites
- 8YF · (2R)-2-[(2S,3R)-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-4-(2-methanimidamidoethylsulfanyl)-2,3-dihydro-1H-pyrrole-5-carboxylic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 12 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 403 | 0.71 | 0.82 | 44 | EDO, ZN, 8YF |
| 2 | 141 | 0.48 | 0.78 | 23 | ZN, 8YF |
| 3 | 101 | 0.40 | 0.77 | 16 | EDO |
| 4 | 54 | 0.36 | 0.79 | 13 | empty |
| 5 | 51 | 0.28 | 0.75 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 783 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6RZR · Structure of IMP-13 metallo-beta-lactamase complexed with hydrolysed imipenem · 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 6RZR · PDBe 6RZR · UniProt Q7WYA8
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