MolNFT v1 · #49670 · protein
GTP cyclohydrolase III from M. jannaschii (MJ0145) complexed with GTP and metal ions
2QV6: “GTP cyclohydrolase III from M. jannaschii (MJ0145) complexed with GTP and metal ions”. X-ray diffraction, 4 ligands (GTP, K, CA), 8 pockets (best druggability 0.75). MolNFT v1 #49670 on GenesisL1: 3D structure, binding sites and…
- 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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