Research workbench
GTP cyclohydrolase III from M. jannaschii (MJ0145) complexed with GTP and metal ions
Analyse GTP cyclohydrolase III from M. jannaschii (MJ0145) complexed with GTP and metal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QV6
- Type
- protein
- Length
- 1,008 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTP cyclohydrolase III
- EC
- 3.5.4.29
- UniProt
- Q57609
- Ligands
- GTP, K, CA, NA
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | GTP cyclohydrolase III (EC 3.5.4.29) | protein | 253 | 44% helix, 23% strand | Q57609 |
| B | GTP cyclohydrolase III (EC 3.5.4.29) | protein | 250 | 45% helix, 23% strand | Q57609 |
| C | GTP cyclohydrolase III (EC 3.5.4.29) | protein | 252 | 44% helix, 23% strand | Q57609 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 4 copies · chains A, C, B, D
- K · Potassium ion · metal · 4 copies · chains A, C, B, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 234 | 0.75 | 0.90 | 36 | K, CA, NA, GTP |
| 2 | 245 | 0.74 | 0.89 | 37 | K, CA, GTP |
| 3 | 235 | 0.74 | 0.89 | 36 | K, CA, GTP |
| 4 | 247 | 0.72 | 0.87 | 41 | K, CA, NA, GTP |
| 5 | 155 | 0.40 | 0.73 | 26 | empty |
Interfaces
6 interfaces between chains.
- A–C · 3195 Ų buried · 46 hydrogen bonds · protein-protein
- B–D · 3185 Ų buried · 44 hydrogen bonds · protein-protein
- B–C · 806 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 802 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 531 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2QV6 · GTP cyclohydrolase III from M. jannaschii (MJ0145) complexed with GTP and metal ions · the same entry in another collection · chain D against D, TM-score 1.00
- Q57609 · AlphaFold monomer V2.0 prediction for GTP cyclohydrolase III (Q57609) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q57609
- Elsewhere: RCSB PDB 2QV6 · PDBe 2QV6 · UniProt Q57609
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