MolNFT v1 · #158497 · protein
Crystal structure of tla-1 extended spectrum beta-lactamase
6NVT: “Crystal structure of tla-1 extended spectrum beta-lactamase”. X-ray diffraction, 2 ligands (SO4, CL), 9 pockets (best druggability 0.73). MolNFT v1 #158497 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6NVT
- Type
- protein
- Length
- 1,104 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q9X6W1
- Ligands
- SO4, CL
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-lactamase (EC 3.5.2.6) | protein | 276 | 45% helix, 20% strand | Q9X6W1 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 30 copies · chains A, B, C, D
- CL · Chloride ion · ion · 8 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 37 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 388 | 0.73 | 0.83 | 36 | empty |
| 2 | 208 | 0.51 | 0.77 | 29 | SO4 |
| 3 | 186 | 0.48 | 0.76 | 22 | ACT |
| 4 | 186 | 0.47 | 0.75 | 36 | SO4 |
| 5 | 155 | 0.47 | 0.77 | 28 | ACT |
Interfaces
2 interfaces between chains.
- B–C · 613 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 513 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6NVT · Crystal structure of TLA-1 extended spectrum Beta-lactamase · 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 Q9X6W1
- Elsewhere: RCSB PDB 6NVT · PDBe 6NVT · UniProt Q9X6W1
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