MolNFT v1 · #148102 · protein
Crystal structure of relp (SAS2) from staphylococcus aureus bound to ampcpp and GTP in the pre-catalytic state
6EWZ · GTP pyrophosphokinase: “Crystal structure of relp (SAS2) from staphylococcus aureus bound to ampcpp and GTP in the pre-catalytic state”. X-ray diffraction, 4 ligands (GTP, APC, MG), 3 pockets (best druggability 0.51). MolNFT v1…
- PDB
- 6EWZ
- Type
- protein
- Length
- 402 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
- GTP, APC, MG, FE
- Pockets
- 3 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTP pyrophosphokinase (EC 2.7.6.5) | protein | 202 | 53% helix, 22% strand | W8U368 |
| B | GTP pyrophosphokinase (EC 2.7.6.5) | protein | 200 | 50% helix, 22% strand | W8U368 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- FE · Fe (III) 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 | 270 | 0.51 | 0.75 | 35 | GTP, APC, MG |
| 2 | 240 | 0.49 | 0.75 | 32 | GTP, APC |
| 3 | 54 | 0.27 | 0.74 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 1360 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 6EWZ · Crystal structure of RelP (SAS2) from Staphylococcus aureus bound to AMPCPP and GTP in… · 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 6EWZ · PDBe 6EWZ · UniProt W8U368
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