Research workbench
Crystal structure of a histidine triad (hit) protein (MFLA_2506) from methylobacillus flagellatus kt at 1.65 a resolution
Analyse Crystal structure of a histidine triad (hit) protein (MFLA_2506) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OIK
- Type
- protein
- Length
- 558 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histidine triad (hit) protein
- UniProt
- Q1GYB6
- Ligands
- ZN, CL
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Histidine triad (hit) protein | protein | 139 | 32% helix, 20% strand | Q1GYB6 |
| C | Histidine triad (hit) protein | protein | 141 | 31% helix, 20% strand | Q1GYB6 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 5 copies · chains A, B, C, D
- GOL · Glycerol · additive · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 759 | 0.70 | 0.77 | 66 | empty |
| 2 | 177 | 0.48 | 0.76 | 26 | CL, GOL |
| 3 | 164 | 0.47 | 0.76 | 25 | CL, GOL |
| 4 | 114 | 0.43 | 0.77 | 24 | CL, GOL |
| 5 | 114 | 0.40 | 0.76 | 24 | CL, GOL |
Interfaces
5 interfaces between chains.
- C–D · 1478 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 1466 Ų buried · 41 hydrogen bonds · protein-protein
- B–D · 228 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 162 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 90 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 modified (engineered).
Compared structures
- 2OIK · Crystal structure of a histidine triad (hit) protein (mfla_2506) from methylobacillus… · 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 Q1GYB6
- Elsewhere: RCSB PDB 2OIK · PDBe 2OIK · UniProt Q1GYB6
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