MolNFT v1 · #67707 · protein
Structure of the class D beta-lactamase oxa-1 in complex with doripenem
3ISG: “Structure of the class D beta-lactamase oxa-1 in complex with doripenem”. X-ray diffraction, 1 ligand (DRW), 3 pockets (best druggability 0.42). MolNFT v1 #67707 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3ISG
- Type
- protein
- Length
- 498 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase oxa-1
- EC
- 3.5.2.6
- UniProt
- P13661
- Ligands
- DRW
- Pockets
- 3 · best druggability 0.42
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-lactamase oxa-1 (EC 3.5.2.6) | protein | 249 | 39% helix, 22% strand | P13661 |
Ligands and binding sites
- DRW · (2S,3R,4S)-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-4-({(3S,5S)-5-[(sulfamoylamino)methyl]pyrrolidin-3-yl}sulfanyl)-3,4-dihydro-2H-pyrrole-5-carboxylic acid · ligand · 2 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 140 | 0.42 | 0.75 | 28 | DRW |
| 2 | 131 | 0.40 | 0.74 | 30 | DRW |
| 3 | 130 | 0.37 | 0.73 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 64 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, carboxylation).
Compared structures
- 3ISG · Structure of the class D beta-lactamase OXA-1 in complex with doripenem · the same entry in another collection · chain A against A, TM-score 1.00
- P13661 · AlphaFold monomer V2.0 prediction for beta-lactamase oxa-1 (P13661) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P13661
- Elsewhere: RCSB PDB 3ISG · PDBe 3ISG · UniProt P13661
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