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Crystal structure of N109P mutant of gatase subunit of methanocaldococcus jannaschii gmp synthetase
Analyse Crystal structure of N109P mutant of 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
- 7D97
- Type
- protein
- Length
- 748 residues
- Chains
- 4
- 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
- Pockets
- 11 · best druggability 0.51
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gmp synthase [glutamine-hydrolyzing] subunit a (EC 6.3.5.2) | protein | 185 | 27% helix, 28% strand | Q58970 |
| B, D | Gmp synthase [glutamine-hydrolyzing] subunit a (EC 6.3.5.2) | protein | 188 | 26% helix, 36% strand | Q58970 |
| C | Gmp synthase [glutamine-hydrolyzing] subunit a (EC 6.3.5.2) | protein | 187 | 27% helix, 30% strand | Q58970 |
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 216 | 0.51 | 0.76 | 34 | empty |
| 2 | 163 | 0.50 | 0.78 | 35 | empty |
| 3 | 181 | 0.47 | 0.75 | 28 | empty |
| 4 | 59 | 0.43 | 0.82 | 23 | empty |
| 5 | 59 | 0.42 | 0.82 | 22 | empty |
Interfaces
5 interfaces between chains.
- A–B · 473 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 348 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 286 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 246 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 142 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7D97 · Crystal structure of N109P mutant of GATase subunit of Methanocaldococcus jannaschii GMP… · the same entry in another collection · chain D against D, 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 A 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 7D97 · PDBe 7D97 · UniProt Q58970
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