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Crystal structure of glycerate kinase (ec 2.7.1.31) (TM1585) from thermotoga maritima at 2.70 a resolution
Analyse Crystal structure of glycerate kinase (ec 2.7.1.31) (TM1585) from thermotoga… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2B8N
- Type
- protein
- Length
- 828 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycerate kinase, putative
- EC
- 2.7.1.31
- UniProt
- Q9X1S1
- Pockets
- 8 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glycerate kinase, putative (EC 2.7.1.31) | protein | 414 | 41% helix, 20% strand | Q9X1S1 |
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 283 | 0.57 | 0.77 | 35 | empty |
| 2 | 246 | 0.53 | 0.76 | 29 | empty |
| 3 | 153 | 0.44 | 0.75 | 24 | empty |
| 4 | 115 | 0.43 | 0.77 | 24 | empty |
| 5 | 104 | 0.43 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1205 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 2B8N · Crystal structure of Glycerate kinase (EC 2.7.1.31) (tm1585) from THERMOTOGA MARITIMA at… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9X1S1 · AlphaFold monomer V2.0 prediction for D-glycerate 2-kinase (Q9X1S1) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9X1S1
- Elsewhere: RCSB PDB 2B8N · PDBe 2B8N · UniProt Q9X1S1
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