MolNFT v1 · #168439 · protein
The crystal structure of a beta-lactamase from shigella flexneri 2A str. 2457T
6WGQ: “The crystal structure of a beta-lactamase from shigella flexneri 2A str. 2457T”. X-ray diffraction, 2 ligands (NI, CL), 6 pockets (best druggability 0.81). MolNFT v1 #168439 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6WGQ
- Type
- protein
- Length
- 717 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- A0A4S3P3Z5
- Ligands
- NI, CL
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 359 | 40% helix, 23% strand | A0A4S3P3Z5 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 358 | 40% helix, 23% strand | A0A4S3P3Z5 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 5 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 13 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 6 copies · chains A, B
- FMT · Formic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 882 | 0.81 | 0.83 | 63 | GOL |
| 2 | 363 | 0.68 | 0.82 | 56 | GOL, CL |
| 3 | 290 | 0.66 | 0.82 | 43 | GOL, CL |
| 4 | 270 | 0.60 | 0.79 | 35 | NI, TRS |
| 5 | 85 | 0.34 | 0.74 | 20 | GOL, FMT |
Interfaces
1 interface between chains.
- A–B · 540 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6WGQ · The crystal structure of a beta-lactamase from Shigella flexneri 2a str. 2457T · 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 A0A4S3P3Z5
- Elsewhere: RCSB PDB 6WGQ · PDBe 6WGQ · UniProt A0A4S3P3Z5
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