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Crsytal structure of a xmp complexed atppase subunit of M. jannaschii gmp synthetase
Analyse Crsytal structure of a xmp complexed atppase subunit of M. jannaschii gmp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JP9
- Type
- protein
- Length
- 1,166 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gmp synthase [glutamine-hydrolyzing] subunit B
- EC
- 6.3.5.2
- UniProt
- Q58531
- Ligands
- XMP
- Pockets
- 13 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gmp synthase [glutamine-hydrolyzing] subunit B (EC 6.3.5.2) | protein | 298 | 43% helix, 23% strand | Q58531 |
| B | Gmp synthase [glutamine-hydrolyzing] subunit B (EC 6.3.5.2) | protein | 296 | 43% helix, 22% strand | Q58531 |
| C | Gmp synthase [glutamine-hydrolyzing] subunit B (EC 6.3.5.2) | protein | 274 | 44% helix, 21% strand | Q58531 |
| D | Gmp synthase [glutamine-hydrolyzing] subunit B (EC 6.3.5.2) | protein | 298 | 43% helix, 21% strand | Q58531 |
Ligands and binding sites
- XMP · Xanthosine-5'-monophosphate · ligand · 4 copies · chains A, B, C, D
- PGE · Triethylene glycol · additive · chains D
- MLA · Malonic acid · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 883 | 0.73 | 0.77 | 70 | empty |
| 2 | 1142 | 0.72 | 0.76 | 114 | MLA |
| 3 | 792 | 0.70 | 0.76 | 72 | XMP |
| 4 | 482 | 0.68 | 0.79 | 66 | empty |
| 5 | 395 | 0.61 | 0.76 | 51 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1717 Ų buried · 51 hydrogen bonds · protein-protein
- C–D · 1678 Ų buried · 47 hydrogen bonds · protein-protein
- B–D · 498 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 312 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 226 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6JP9 · Crsytal structure of a XMP complexed ATPPase subunit of M. jannaschii GMP synthetase · the same entry in another collection · chain D against D, TM-score 1.00
- Q58531 · AlphaFold monomer V2.0 prediction for gmp synthase [glutamine- hydrolyzing] subunit B… · a predicted model of the same protein · chain D 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 Q58531
- Elsewhere: RCSB PDB 6JP9 · PDBe 6JP9 · UniProt Q58531
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