MolNFT v1 · #105968 · protein
Crystal structure of GTP cyclohydrolase II from helicobacter pylori 26695
4RL4 · GTP cyclohydrolase-2: “Crystal structure of GTP cyclohydrolase II from helicobacter pylori 26695”. X-ray diffraction, 1 ligand (PPV), 4 pockets (best druggability 0.65). MolNFT v1 #105968 on GenesisL1: 3D structure, binding sites…
- PDB
- 4RL4
- Type
- protein
- Length
- 346 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTP cyclohydrolase-2
- EC
- 3.5.4.25
- UniProt
- O08315
- Ligands
- PPV
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTP cyclohydrolase-2 (EC 3.5.4.25) | protein | 173 | 32% helix, 30% strand | O08315 |
| B | GTP cyclohydrolase-2 (EC 3.5.4.25) | protein | 173 | 31% helix, 28% strand | O08315 |
Ligands and binding sites
- PPV · Pyrophosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 345 | 0.65 | 0.80 | 43 | empty |
| 2 | 350 | 0.64 | 0.79 | 35 | PPV |
| 3 | 361 | 0.63 | 0.79 | 40 | PPV |
| 4 | 129 | 0.55 | 0.83 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1868 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4RL4 · Crystal structure of GTP cyclohydrolase II from Helicobacter pylori 26695 · the same entry in another collection · chain A against A, TM-score 1.00
- O08315 · AlphaFold monomer V2.0 prediction for GTP cyclohydrolase-2 (O08315) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 O08315
- Elsewhere: RCSB PDB 4RL4 · PDBe 4RL4 · UniProt O08315
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