MolNFT v1 · #166913 · protein
The crystal structure of a beta-lactamase from chitinophaga pinensis dsm 2588
6V4W: “The crystal structure of a beta-lactamase from chitinophaga pinensis dsm 2588”. X-ray diffraction, 1 ligand (CL), 3 pockets (best druggability 0.72). MolNFT v1 #166913 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6V4W
- Type
- protein
- Length
- 544 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- C7PRN9
- Ligands
- CL
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 274 | 47% helix, 21% strand | C7PRN9 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 270 | 46% helix, 21% strand | C7PRN9 |
Ligands and binding sites
- CL · Chloride ion · ion · 8 copies · chains A, B
- ACT · Acetate ion · additive · 3 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains B
- FMT · Formic acid · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 728 | 0.72 | 0.78 | 81 | CL, MES |
| 2 | 202 | 0.48 | 0.76 | 26 | ACT |
| 3 | 78 | 0.39 | 0.78 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 677 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 6V4W · The crystal structure of a beta-lactamase from Chitinophaga pinensis DSM 2588 · 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 C7PRN9
- Elsewhere: RCSB PDB 6V4W · PDBe 6V4W · UniProt C7PRN9
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