MolNFT v1 · #118636 · protein
Imipenem complex of the ges-5 C69G mutant
5F83 · Beta-lactamase: “Imipenem complex of the ges-5 C69G mutant”. X-ray diffraction, 1 ligand (IM2), 7 pockets (best druggability 0.73). MolNFT v1 #118636 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5F83
- Type
- protein
- Length
- 534 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q0Z8S4
- Ligands
- IM2
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 268 | 49% helix, 19% strand | Q0Z8S4 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 266 | 49% helix, 19% strand | Q0Z8S4 |
Ligands and binding sites
- IM2 · (5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carbox ylic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 541 | 0.73 | 0.81 | 50 | empty |
| 2 | 81 | 0.47 | 0.82 | 17 | empty |
| 3 | 70 | 0.39 | 0.79 | 24 | empty |
| 4 | 85 | 0.39 | 0.77 | 16 | empty |
| 5 | 62 | 0.38 | 0.80 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 911 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5F83 · Imipenem complex of the GES-5 C69G mutant · 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 Q0Z8S4
- Elsewhere: RCSB PDB 5F83 · PDBe 5F83 · UniProt Q0Z8S4
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