Research workbench
Crystal structure of a histidine triad (hit) protein (SMC02904) from sinorhizobium meliloti 1021 at 2.06 a resolution
Analyse Crystal structure of a histidine triad (hit) protein (SMC02904) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NRD
- Type
- protein
- Length
- 538 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histidine triad (hit) protein
- UniProt
- Q92KT3
- Ligands
- SO4
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Histidine triad (hit) protein | protein | 135 | 36% helix, 22% strand | Q92KT3 |
| B, C | Histidine triad (hit) protein | protein | 134 | 34% helix, 23% strand | Q92KT3 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 13 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 137 | 0.82 | 0.99 | 20 | empty |
| 2 | 133 | 0.82 | 0.99 | 20 | GOL |
| 3 | 54 | 0.68 | 0.96 | 22 | empty |
| 4 | 184 | 0.59 | 0.82 | 30 | SO4 |
| 5 | 217 | 0.59 | 0.80 | 27 | SO4 |
Interfaces
3 interfaces between chains.
- A–B · 1352 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 1351 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 732 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 3NRD · Crystal structure of a histidine triad (HIT) protein (SMc02904) from SINORHIZOBIUM… · 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 Q92KT3
- Elsewhere: RCSB PDB 3NRD · PDBe 3NRD · UniProt Q92KT3
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