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Crystal structure of a gmp synthase (glutamine-hydrolyzing) from neisseria gonorrhoeae
Analyse Crystal structure of a gmp synthase (glutamine-hydrolyzing) from neisseria… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TW7
- Type
- protein
- Length
- 2,942 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gmp synthase [glutamine-hydrolyzing]
- EC
- 6.3.5.2
- UniProt
- B4RJH7
- Ligands
- MG
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 6 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gmp synthase [glutamine-hydrolyzing] (EC 6.3.5.2) | protein | 490 | 37% helix, 26% strand | B4RJH7 |
| B | Gmp synthase [glutamine-hydrolyzing] (EC 6.3.5.2) | protein | 490 | 36% helix, 25% strand | B4RJH7 |
| C | Gmp synthase [glutamine-hydrolyzing] (EC 6.3.5.2) | protein | 492 | 36% helix, 26% strand | B4RJH7 |
| D | Gmp synthase [glutamine-hydrolyzing] (EC 6.3.5.2) | protein | 491 | 36% helix, 25% strand | B4RJH7 |
| E | Gmp synthase [glutamine-hydrolyzing] (EC 6.3.5.2) | protein | 489 | 36% helix, 26% strand | B4RJH7 |
| F | Gmp synthase [glutamine-hydrolyzing] (EC 6.3.5.2) | protein | 490 | 37% helix, 25% strand | B4RJH7 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 848 | 0.72 | 0.77 | 62 | empty |
| 2 | 775 | 0.66 | 0.74 | 55 | empty |
| 3 | 351 | 0.61 | 0.78 | 47 | empty |
| 4 | 337 | 0.61 | 0.78 | 46 | empty |
| 5 | 337 | 0.60 | 0.77 | 48 | empty |
Interfaces
7 interfaces between chains.
- B–E · 1728 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 1720 Ų buried · 29 hydrogen bonds · protein-protein
- C–F · 1648 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 394 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 321 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5TW7 · Crystal structure of a GMP synthase (glutamine-hydrolyzing) from Neisseria gonorrhoeae · the same entry in another collection · chain F against F, TM-score 1.00
- B4RJH7 · AlphaFold monomer V2.0 prediction for gmp synthase [glutamine- hydrolyzing] (B4RJH7) · a predicted model of the same protein · chain E 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 B4RJH7
- Elsewhere: RCSB PDB 5TW7 · PDBe 5TW7 · UniProt B4RJH7
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