MolNFT v1 · #8082 · protein
Proclavaminate amidino hydrolase from streptomyces clavuligerus
1GQ7: “Proclavaminate amidino hydrolase from streptomyces clavuligerus”. X-ray diffraction, 1 ligand (MN), 17 pockets (best druggability 0.81). MolNFT v1 #8082 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1GQ7
- Type
- protein
- Length
- 1,806 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proclavaminate amidino hydrolase
- EC
- 3.5.3.11
- UniProt
- P37819
- Ligands
- MN
- Pockets
- 17 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Proclavaminate amidino hydrolase (EC 3.5.3.11) | protein | 301 | 42% helix, 20% strand | P37819 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 12 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 612 | 0.81 | 0.86 | 49 | empty |
| 2 | 586 | 0.81 | 0.87 | 41 | empty |
| 3 | 568 | 0.81 | 0.87 | 40 | empty |
| 4 | 931 | 0.78 | 0.80 | 114 | empty |
| 5 | 593 | 0.74 | 0.81 | 73 | empty |
Interfaces
12 interfaces between chains.
- B–C · 1180 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 1176 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 1161 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1160 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1157 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 1GQ7 · Proclavaminate amidino hydrolase from streptomyces clavuligerus · the same entry in another collection · chain B against B, 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 P37819
- Elsewhere: RCSB PDB 1GQ7 · PDBe 1GQ7 · UniProt P37819
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