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Crystal structure of acivicin-bound gatase subunit of methanocaldococcus jannaschii gmp synthetase
Analyse Crystal structure of acivicin-bound gatase subunit of methanocaldococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7D95
- 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
- 1 · best druggability 0.42
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
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 132 | 0.42 | 0.75 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 326 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 2 modified (covalent ligand, nonstandard).
Compared structures
- 7D95 · Crystal structure of acivicin-bound GATase subunit of Methanocaldococcus jannaschii GMP… · 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 7D95 · PDBe 7D95 · UniProt Q58970
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