MolNFT v1 · #124244 · protein
Crystal structure of GTP cyclohydrolase-ib with tris
5K9G · GTP cyclohydrolase FOLE2: “Crystal structure of GTP cyclohydrolase-ib with tris”. X-ray diffraction, 1 ligand (ZN), 7 pockets (best druggability 0.53). MolNFT v1 #124244 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5K9G
- Type
- protein
- Length
- 488 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTP cyclohydrolase FOLE2
- EC
- 3.5.4.16
- UniProt
- Q5F9K6
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTP cyclohydrolase FOLE2 (EC 3.5.4.16) | protein | 245 | 27% helix, 45% strand | Q5F9K6 |
| B | GTP cyclohydrolase FOLE2 (EC 3.5.4.16) | protein | 243 | 27% helix, 45% strand | Q5F9K6 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B
- FMT · Formic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.53 | 0.88 | 17 | empty |
| 2 | 55 | 0.53 | 0.88 | 17 | empty |
| 3 | 115 | 0.49 | 0.80 | 26 | ZN, TRS, FMT |
| 4 | 122 | 0.49 | 0.79 | 25 | ZN |
| 5 | 53 | 0.37 | 0.80 | 13 | EDO |
Interfaces
1 interface between chains.
- A–B · 1660 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
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 Q5F9K6
- Elsewhere: RCSB PDB 5K9G · PDBe 5K9G · UniProt Q5F9K6
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