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Crystal structure of a putative gmp synthase subunit a protein (TA0944M) from thermoplasma acidophilum at 2.45 a resolution
Analyse Crystal structure of a putative gmp synthase subunit a protein (TA0944M) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2A9V
- Type
- protein
- Length
- 796 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gmp synthase
- EC
- 6.3.5.2
- UniProt
- Q9HJM3
- Ligands
- SCN, CL
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gmp synthase (EC 6.3.5.2) | protein | 199 | 30% helix, 33% strand | Q9HJM3 |
| B | Gmp synthase (EC 6.3.5.2) | protein | 197 | 31% helix, 31% strand | Q9HJM3 |
| C | Gmp synthase (EC 6.3.5.2) | protein | 199 | 30% helix, 31% strand | Q9HJM3 |
| D | Gmp synthase (EC 6.3.5.2) | protein | 201 | 31% helix, 33% strand | Q9HJM3 |
Ligands and binding sites
- SCN · Thiocyanate ion · ion · 5 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains B
- GOL · Glycerol · additive · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 434 | 0.67 | 0.80 | 58 | GOL |
| 2 | 258 | 0.63 | 0.81 | 41 | SCN, GOL |
| 3 | 406 | 0.61 | 0.77 | 46 | empty |
| 4 | 110 | 0.43 | 0.78 | 29 | empty |
| 5 | 60 | 0.41 | 0.82 | 15 | GOL |
Interfaces
5 interfaces between chains.
- B–C · 717 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 528 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 148 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 69 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 11 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 2A9V · Crystal structure of a putative gmp synthase subunit a protein (ta0944m) from… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9HJM3 · AlphaFold monomer V2.0 prediction for gmp synthase [glutamine- hydrolyzing] subunit a… · a predicted model of the same protein · chain B 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 Q9HJM3
- Elsewhere: RCSB PDB 2A9V · PDBe 2A9V · UniProt Q9HJM3
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