MolNFT v1 · #175863 · protein
Crystal structure of gatase subunit of methanocaldococcus jannaschii gmp synthetase
7D40 · Gmp synthase [glutamine-hydrolyzing] subunit a: “Crystal structure of gatase subunit of methanocaldococcus jannaschii gmp synthetase”. X-ray diffraction, 1 ligand (SNN), 3 pockets (best druggability 0.44). MolNFT v1 #175863 on…
- PDB
- 7D40
- Type
- protein
- Length
- 374 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gmp synthase [glutamine-hydrolyzing] subunit a
- EC
- 6.3.5.2
- UniProt
- Q58970
- Ligands
- SNN
- Pockets
- 3 · best druggability 0.44
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Gmp synthase [glutamine-hydrolyzing] subunit a (EC 6.3.5.2) | protein | 187 | 25% helix, 29% strand | Q58970 |
Ligands and binding sites
- SNN · L-3-aminosuccinimide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 107 | 0.44 | 0.78 | 29 | empty |
| 2 | 70 | 0.40 | 0.79 | 24 | empty |
| 3 | 78 | 0.37 | 0.77 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 341 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 7D40 · Crystal structure of GATase subunit of Methanocaldococcus jannaschii GMP synthetase · the same entry in another collection · chain A against A, TM-score 1.00
- Q58970 · 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 0.98
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 Q58970
- Elsewhere: RCSB PDB 7D40 · PDBe 7D40 · UniProt Q58970
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