MolNFT v1 · #131659 · protein
Oxa-48 in complex with substrate imipenem
5QB4 · Beta-lactamase: “Oxa-48 in complex with substrate imipenem”. X-ray diffraction, 2 ligands (IM2, CL), 9 pockets (best druggability 0.78). MolNFT v1 #131659 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5QB4
- Type
- protein
- Length
- 968 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q6XEC0
- Ligands
- IM2, CL
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-lactamase (EC 3.5.2.6) | protein | 242 | 41% helix, 21% strand | Q6XEC0 |
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 · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains C, D
- EDO · 1,2-ethanediol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1072 | 0.78 | 0.80 | 98 | EDO |
| 2 | 861 | 0.76 | 0.80 | 99 | IM2 |
| 3 | 189 | 0.50 | 0.77 | 26 | empty |
| 4 | 112 | 0.36 | 0.73 | 22 | IM2 |
| 5 | 50 | 0.35 | 0.79 | 18 | empty |
Interfaces
4 interfaces between chains.
- A–B · 513 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 348 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 294 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 260 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 4 modified (covalent ligand, carboxylation).
Compared structures
- 5QB4 · Oxa-48 in complex with substrate 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 Q6XEC0
- Elsewhere: RCSB PDB 5QB4 · PDBe 5QB4 · UniProt Q6XEC0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.