MolNFT v1 · #158500 · protein
Crystal structure of penicillin G acylase from bacillus sp. fjat-27231
6NVX · Penicillin G acylase, alpha-subunit: “Crystal structure of penicillin G acylase from bacillus sp. fjat-27231”. X-ray diffraction, 1 ligand (CA), 7 pockets (best druggability 0.73). MolNFT v1 #158500 on GenesisL1: 3D structure…
- PDB
- 6NVX
- Type
- protein
- Length
- 730 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin G acylase, alpha-subunit; Penicillin G acylase, beta-subunit
- UniProt
- A0A0K9H482
- Ligands
- CA
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin G acylase, alpha-subunit | protein | 203 | 67% helix, 7% strand | A0A0K9H482 |
| B | Penicillin G acylase, beta-subunit | protein | 527 | 31% helix, 28% strand | A0A0K9H482 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains B, A
- GOL · Glycerol · additive · 6 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 619 | 0.73 | 0.80 | 81 | GOL |
| 2 | 184 | 0.45 | 0.74 | 16 | empty |
| 3 | 138 | 0.42 | 0.75 | 22 | empty |
| 4 | 63 | 0.36 | 0.78 | 19 | GOL |
| 5 | 96 | 0.35 | 0.74 | 15 | GOL |
Interfaces
1 interface between chains.
- A–B · 6307 Ų buried · 101 hydrogen bonds · protein-protein
Compared structures
- 6NVX · Crystal structure of penicillin G acylase from Bacillus sp. FJAT-27231 · 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 A0A0K9H482
- Elsewhere: RCSB PDB 6NVX · PDBe 6NVX · UniProt A0A0K9H482
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