MolNFT v1 · #158056 · protein
Crystal structure of the putative class a beta-lactamase penp from rhodopseudomonas palustris
6NIQ: “Crystal structure of the putative class a beta-lactamase penp from rhodopseudomonas palustris”. X-ray diffraction, 1 ligand (CL), 4 pockets (best druggability 0.63). MolNFT v1 #158056 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6NIQ
- Type
- protein
- Length
- 524 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q6NCV7
- Ligands
- CL
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 263 | 45% helix, 18% strand | Q6NCV7 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 261 | 43% helix, 18% strand | Q6NCV7 |
Ligands and binding sites
- CL · Chloride ion · ion · 3 copies · chains A, B
- FMT · Formic acid · additive · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 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 | 0.63 | 0.76 | 61 | PEG |
| 2 | 50 | 0.29 | 0.75 | 13 | empty |
| 3 | 70 | 0.29 | 0.74 | 18 | EDO, FMT |
| 4 | 64 | 0.28 | 0.74 | 16 | FMT, EDO |
Interfaces
1 interface between chains.
- A–B · 687 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6NIQ · Crystal Structure of the Putative Class A Beta-Lactamase PenP from Rhodopseudomonas… · 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 Q6NCV7
- Elsewhere: RCSB PDB 6NIQ · PDBe 6NIQ · UniProt Q6NCV7
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