MolNFT v1 · #148103 · protein
Crystal structure of relp (SAS2) from staphylococcus aureus bound to pppgpp in the post-catalytic state
6EX0 · GTP pyrophosphokinase: “Crystal structure of relp (SAS2) from staphylococcus aureus bound to pppgpp in the post-catalytic state”. X-ray diffraction, 2 ligands (C1Z, FE2), 3 pockets (best druggability 0.51). MolNFT v1 #148103 on…
- PDB
- 6EX0
- Type
- protein
- Length
- 391 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTP pyrophosphokinase
- EC
- 2.7.6.5
- UniProt
- W8U368
- Ligands
- C1Z, FE2
- Pockets
- 3 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTP pyrophosphokinase (EC 2.7.6.5) | protein | 194 | 53% helix, 23% strand | W8U368 |
| B | GTP pyrophosphokinase (EC 2.7.6.5) | protein | 197 | 51% helix, 22% strand | W8U368 |
Ligands and binding sites
- C1Z · Guanosine 3'-diphosphate 5'-triphosphate · ligand · 2 copies · chains A, B
- FE2 · Fe (II) ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 252 | 0.51 | 0.75 | 33 | C1Z |
| 2 | 116 | 0.38 | 0.75 | 25 | C1Z |
| 3 | 53 | 0.28 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1327 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6EX0 · Crystal structure of RelP (SAS2) from Staphylococcus aureus bound to pppGpp in the… · 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 W8U368
- Elsewhere: RCSB PDB 6EX0 · PDBe 6EX0 · UniProt W8U368
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