MolNFT v1 · #15405 · protein
Biosynthesis of pteridins. reaction mechanism of GTP cyclohydrolase I
1N3S: “Biosynthesis of pteridins. reaction mechanism of GTP cyclohydrolase I”. X-ray diffraction, 1 ligand (GTP), 20 pockets (best druggability 0.84). MolNFT v1 #15405 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1N3S
- Type
- protein
- Length
- 2,210 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTP cyclohydrolase I
- EC
- 3.5.4.16
- UniProt
- P0A6T5
- Ligands
- GTP
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J | GTP cyclohydrolase I (EC 3.5.4.16) | protein | 221 | 38% helix, 21% strand | P0A6T5 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 10 copies · chains A, E, B, C, D, F, J, G, H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1160 | 0.84 | 0.85 | 139 | empty |
| 2 | 1030 | 0.84 | 0.85 | 127 | empty |
| 3 | 52 | 0.64 | 0.94 | 19 | empty |
| 4 | 224 | 0.62 | 0.81 | 29 | GTP |
| 5 | 205 | 0.62 | 0.82 | 34 | GTP |
Interfaces
10 interfaces between chains.
- I–J · 1343 Ų buried · 36 hydrogen bonds · protein-protein
- G–H · 1333 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 1327 Ų buried · 31 hydrogen bonds · protein-protein
- F–G · 1317 Ų buried · 35 hydrogen bonds · protein-protein
- H–I · 1315 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1N3S · Biosynthesis of pteridins. Reaction mechanism of GTP cyclohydrolase I · the same entry in another collection · chain J against J, TM-score 1.00
- P0A6T5 · AlphaFold monomer V2.0 prediction for GTP cyclohydrolase 1 (P0A6T5) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P0A6T5
- Elsewhere: RCSB PDB 1N3S · PDBe 1N3S · UniProt P0A6T5
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