MolNFT v1 · #158501 · protein
Crystal structure of penicillin G acylase from bacillus thermotolerans
6NVY: “Crystal structure of penicillin G acylase from bacillus thermotolerans”. X-ray diffraction, 1 ligand (CA), 16 pockets (best druggability 0.72). MolNFT v1 #158501 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6NVY
- Type
- protein
- Length
- 1,454 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin G acylase
- UniProt
- A0A0F5I5V4
- Ligands
- CA
- Pockets
- 16 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Penicillin G acylase | protein | 191 | 68% helix, 6% strand | A0A0F5I5V4 |
| B, D | Penicillin G acylase | protein | 536 | 28% helix, 29% strand | A0A0F5I5V4 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 765 | 0.72 | 0.78 | 90 | empty |
| 2 | 671 | 0.70 | 0.78 | 62 | empty |
| 3 | 230 | 0.64 | 0.83 | 29 | empty |
| 4 | 170 | 0.45 | 0.75 | 31 | empty |
| 5 | 168 | 0.44 | 0.74 | 23 | empty |
Interfaces
5 interfaces between chains.
- A–B · 6707 Ų buried · 111 hydrogen bonds · protein-protein
- C–D · 6625 Ų buried · 112 hydrogen bonds · protein-protein
- B–C · 319 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 108 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 12 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6NVY · Crystal structure of penicillin G acylase from Bacillus thermotolerans · 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 A0A0F5I5V4
- Elsewhere: RCSB PDB 6NVY · PDBe 6NVY · UniProt A0A0F5I5V4
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