MolNFT v1 · #165354 · protein
Crystal structure of ges-5 carbapenemase
6TS9 · Beta-lactamase: “Crystal structure of ges-5 carbapenemase”. X-ray diffraction, 1 ligand (BR), 7 pockets (best druggability 0.73). MolNFT v1 #165354 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6TS9
- Type
- protein
- Length
- 537 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q09HD0
- Ligands
- BR
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 268 | 48% helix, 19% strand | Q09HD0 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 269 | 49% helix, 19% strand | Q09HD0 |
Ligands and binding sites
- BR · Bromide ion · ion · 4 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 2 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
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 | 498 | 0.73 | 0.81 | 43 | empty |
| 2 | 123 | 0.45 | 0.78 | 18 | empty |
| 3 | 103 | 0.45 | 0.79 | 18 | empty |
| 4 | 71 | 0.37 | 0.78 | 19 | empty |
| 5 | 64 | 0.33 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 902 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6TS9 · Crystal structure 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 6TS9 · PDBe 6TS9 · UniProt Q09HD0
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