Research workbench
Structure of paenibacillus polymyxa gs bound to met-sox-P-ADP (transition state complex) to 1.98 angstom
Analyse Structure of paenibacillus polymyxa gs bound to met-sox-P-ADP (transition state… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TDP
- Type
- protein
- Length
- 1,317 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamine synthetase
- EC
- 6.3.1.2
- UniProt
- A0A0F0G8G2
- Ligands
- ADP, P3S, MG
- Pockets
- 14 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamine synthetase (EC 6.3.1.2) | protein | 439 | 38% helix, 24% strand | A0A0F0G8G2 |
| C | Glutamine synthetase (EC 6.3.1.2) | protein | 440 | 38% helix, 23% strand | A0A0F0G8G2 |
| B | Glutamine synthetase (EC 6.3.1.2) | protein | 438 | 38% helix, 23% strand | A0A0F0G8G2 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains A, C, B
- P3S · L-methionine-S-sulfoximine phosphate · ligand · 3 copies · chains A, C, B
- MG · Magnesium ion · metal · 9 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 394 | 0.79 | 0.88 | 53 | ADP, P3S, MG |
| 2 | 375 | 0.78 | 0.88 | 52 | ADP, P3S, MG |
| 3 | 402 | 0.64 | 0.78 | 50 | empty |
| 4 | 383 | 0.61 | 0.77 | 45 | empty |
| 5 | 196 | 0.59 | 0.81 | 41 | ADP, P3S, MG |
Interfaces
2 interfaces between chains.
- C–B · 1466 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 1458 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 7TDP · Structure of Paenibacillus polymyxa GS bound to Met-Sox-P-ADP (Transition state complex)… · 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 A0A0F0G8G2
- Elsewhere: RCSB PDB 7TDP · PDBe 7TDP · UniProt A0A0F0G8G2
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