Research workbench
Ges-2 ertapenem acyl-enzyme complex
Analyse Ges-2 ertapenem acyl-enzyme complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QU3
- Type
- protein
- Length
- 533 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase ges-2
- UniProt
- Q93F76
- Ligands
- 1RG, CA, IOD
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase ges-2 | protein | 268 | 49% helix, 19% strand | Q93F76 |
| B | Beta-lactamase ges-2 | protein | 265 | 48% helix, 19% strand | Q93F76 |
Ligands and binding sites
- 1RG · (4R,5S)-3-({(3S,5S)-5-[(3-carboxyphenyl) carbamoyl]pyrrolidin-3-yl}sulfanyl)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-4-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · chains A
- IOD · Iodide ion · ion · 6 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains 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 | 533 | 0.72 | 0.81 | 49 | empty |
| 2 | 77 | 0.42 | 0.80 | 26 | empty |
| 3 | 92 | 0.40 | 0.77 | 18 | empty |
| 4 | 70 | 0.38 | 0.78 | 24 | empty |
| 5 | 77 | 0.30 | 0.74 | 16 | 1RG |
Interfaces
1 interface between chains.
- A–B · 910 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 4QU3 · GES-2 ertapenem acyl-enzyme complex · the same entry in another collection · chain B against B, 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 Q93F76
- Elsewhere: RCSB PDB 4QU3 · PDBe 4QU3 · UniProt Q93F76
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