Research workbench
Proclavaminate amidino hydrolase from streptomyces clavuligerus
Analyse Proclavaminate amidino hydrolase from streptomyces clavuligerus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GQ6
- Type
- protein
- Length
- 888 residues
- Chains
- 3
- 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
- 5 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proclavaminate amidino hydrolase (EC 3.5.3.11) | protein | 295 | 42% helix, 21% strand | P37819 |
| B | Proclavaminate amidino hydrolase (EC 3.5.3.11) | protein | 301 | 41% helix, 20% strand | P37819 |
| C | Proclavaminate amidino hydrolase (EC 3.5.3.11) | protein | 292 | 42% helix, 21% strand | P37819 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 519 | 0.70 | 0.80 | 73 | empty |
| 2 | 341 | 0.69 | 0.82 | 44 | empty |
| 3 | 267 | 0.59 | 0.79 | 36 | empty |
| 4 | 213 | 0.59 | 0.81 | 37 | empty |
| 5 | 108 | 0.34 | 0.73 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1048 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1035 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1021 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 1GQ6 · Proclavaminate amidino hydrolase from streptomyces clavuligerus · 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 P37819
- Elsewhere: RCSB PDB 1GQ6 · PDBe 1GQ6 · UniProt P37819
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