Research workbench
Structure of GTP cyclohydrolase I from thermus thermophilus HB8
Analyse Structure of GTP cyclohydrolase I from thermus thermophilus HB8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WM9
- Type
- protein
- Length
- 924 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTP cyclohydrolase I
- EC
- 3.5.4.16
- UniProt
- Q5SH52
- Ligands
- ZN
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | GTP cyclohydrolase I (EC 3.5.4.16) | protein | 185 | 43% helix, 27% strand | Q5SH52 |
| E | GTP cyclohydrolase I (EC 3.5.4.16) | protein | 184 | 46% helix, 27% strand | Q5SH52 |
Ligands and binding sites
- ZN · Zinc ion · metal · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 692 | 0.79 | 0.84 | 72 | empty |
| 2 | 75 | 0.64 | 0.92 | 22 | empty |
| 3 | 86 | 0.62 | 0.89 | 25 | ZN |
| 4 | 84 | 0.61 | 0.89 | 23 | empty |
| 5 | 80 | 0.60 | 0.89 | 26 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1314 Ų buried · 18 hydrogen bonds · protein-protein
- A–E · 1310 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1284 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1281 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 1242 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 1WM9 · Structure of GTP cyclohydrolase I from Thermus thermophilus HB8 · 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 Q5SH52
- Elsewhere: RCSB PDB 1WM9 · PDBe 1WM9 · UniProt Q5SH52
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