Research workbench
Crystal structure of a putative yfit-like metal-dependent hydrolase (BH0186) from bacillus halodurans C-125 at 2.30 a resolution
Analyse Crystal structure of a putative yfit-like metal-dependent hydrolase (BH0186)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2RD9
- Type
- protein
- Length
- 748 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BH0186 protein
- UniProt
- Q9KGB8
- Ligands
- NI
- Pockets
- 12 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 61% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | BH0186 protein | protein | 189 | 61% helix, 7% strand | Q9KGB8 |
| B | BH0186 protein | protein | 184 | 61% helix, 6% strand | Q9KGB8 |
| C | BH0186 protein | protein | 186 | 60% helix, 6% strand | Q9KGB8 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 4 copies · chains A, D, B, C
- GOL · Glycerol · additive · 7 copies · chains A, D, B, C
- IMD · Imidazole · additive · 5 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1085 | 0.70 | 0.75 | 76 | empty |
| 2 | 708 | 0.66 | 0.75 | 54 | empty |
| 3 | 329 | 0.52 | 0.73 | 28 | empty |
| 4 | 173 | 0.51 | 0.78 | 21 | GOL |
| 5 | 132 | 0.49 | 0.79 | 18 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3213 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 3176 Ų buried · 39 hydrogen bonds · protein-protein
- A–D · 1539 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 1350 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 743 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 2RD9 · Crystal structure of a putative yfit-like metal-dependent hydrolase (bh0186) from… · 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 Q9KGB8
- Elsewhere: RCSB PDB 2RD9 · PDBe 2RD9 · UniProt Q9KGB8
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