Research workbench
Crystal structure of putative had family hydrolase from streptomyces avermitilis ma-4680
Analyse Crystal structure of putative had family hydrolase from streptomyces… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MMZ
- Type
- protein
- Length
- 662 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative had family hydrolase
- UniProt
- Q82HY3
- Ligands
- CA, CL
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative had family hydrolase | protein | 163 | 40% helix, 20% strand | Q82HY3 |
| C | Putative had family hydrolase | protein | 162 | 37% helix, 17% strand | Q82HY3 |
| D | Putative had family hydrolase | protein | 174 | 35% helix, 19% strand | Q82HY3 |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains A, D, B, C
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 754 | 0.68 | 0.76 | 60 | empty |
| 2 | 230 | 0.57 | 0.79 | 28 | CL, CA |
| 3 | 205 | 0.56 | 0.79 | 38 | CL, CA |
| 4 | 62 | 0.27 | 0.73 | 17 | empty |
Interfaces
4 interfaces between chains.
- B–D · 880 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 862 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 711 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 632 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 3MMZ · CRYSTAL STRUCTURE OF putative HAD family hydrolase from Streptomyces avermitilis MA-4680 · 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 Q82HY3
- Elsewhere: RCSB PDB 3MMZ · PDBe 3MMZ · UniProt Q82HY3
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