Research workbench
Crystal structure of a gmp synthase from acinetobacter baumannii AB5075-uw
Analyse Crystal structure of a gmp synthase from acinetobacter baumannii AB5075-uw in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SBC
- Type
- protein
- Length
- 2,011 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gmp synthase [glutamine-hydrolyzing]
- EC
- 6.3.5.2
- UniProt
- A0A0R1BBX7
- Ligands
- MG, CL, PO4
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gmp synthase [glutamine-hydrolyzing] (EC 6.3.5.2) | protein | 499 | 37% helix, 24% strand | A0A0R1BBX7 |
| B | Gmp synthase [glutamine-hydrolyzing] (EC 6.3.5.2) | protein | 504 | 36% helix, 24% strand | A0A0R1BBX7 |
| C | Gmp synthase [glutamine-hydrolyzing] (EC 6.3.5.2) | protein | 505 | 35% helix, 24% strand | A0A0R1BBX7 |
| D | Gmp synthase [glutamine-hydrolyzing] (EC 6.3.5.2) | protein | 503 | 36% helix, 23% strand | A0A0R1BBX7 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains B, D
- CL · Chloride ion · ion · 12 copies · chains A, D, B, C
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 481 | 0.87 | 0.93 | 46 | empty |
| 2 | 850 | 0.85 | 0.88 | 119 | CL |
| 3 | 737 | 0.85 | 0.89 | 88 | empty |
| 4 | 640 | 0.85 | 0.89 | 87 | CL |
| 5 | 743 | 0.85 | 0.88 | 92 | CL |
Interfaces
6 interfaces between chains.
- B–C · 2203 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 2172 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 1774 Ų buried · 39 hydrogen bonds · protein-protein
- B–D · 1752 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 49 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7SBC · Crystal structure of a GMP synthase from Acinetobacter baumannii AB5075-UW · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A0R1BBX7
- Elsewhere: RCSB PDB 7SBC · PDBe 7SBC · UniProt A0A0R1BBX7
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