Research workbench
Imipenem complex of ges-5 carbapenemase
Analyse Imipenem complex of ges-5 carbapenemase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4H8R
- Type
- protein
- Length
- 533 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Extended-spectrum beta-lactamase ges-5
- UniProt
- Q09HD0
- Ligands
- IM2, NA, IOD
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Extended-spectrum beta-lactamase ges-5 | protein | 267 | 49% helix, 19% strand | Q09HD0 |
| B | Extended-spectrum beta-lactamase ges-5 | protein | 266 | 48% helix, 19% strand | Q09HD0 |
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
- NA · Sodium ion · metal · 4 copies · chains A, B
- IOD · Iodide ion · ion · 17 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 513 | 0.72 | 0.81 | 47 | NA |
| 2 | 107 | 0.46 | 0.79 | 18 | empty |
| 3 | 79 | 0.43 | 0.80 | 26 | empty |
| 4 | 87 | 0.38 | 0.76 | 16 | empty |
| 5 | 69 | 0.37 | 0.78 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 895 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 disulfide (covalent ligand, disulfide).
Compared structures
- 4H8R · Imipenem complex of GES-5 carbapenemase · 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 Q09HD0
- Elsewhere: RCSB PDB 4H8R · PDBe 4H8R · UniProt Q09HD0
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