Research workbench
Crystal structure of manganese-metallated GTP cyclohydrolase type ib
Analyse Crystal structure of manganese-metallated GTP cyclohydrolase type ib in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D2O
- Type
- protein
- Length
- 487 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- UPF0343 protein NGO0387
- EC
- 3.5.4.16
- UniProt
- Q5F9K6
- Ligands
- MN, LI, CL, AZI
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | UPF0343 protein NGO0387 (EC 3.5.4.16) | protein | 244 | 27% helix, 45% strand | Q5F9K6 |
| B | UPF0343 protein NGO0387 (EC 3.5.4.16) | protein | 243 | 27% helix, 45% strand | Q5F9K6 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- LI · Lithium ion · metal · chains B
- CL · Chloride ion · ion · chains B
- AZI · Azide ion · ion · chains A, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 93 | 0.71 | 0.94 | 23 | empty |
| 2 | 95 | 0.69 | 0.93 | 22 | empty |
| 3 | 56 | 0.51 | 0.87 | 16 | empty |
| 4 | 111 | 0.47 | 0.79 | 27 | MN, AZI |
| 5 | 116 | 0.46 | 0.79 | 28 | MN |
Interfaces
1 interface between chains.
- A–B · 1653 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 3D2O · Crystal Structure of Manganese-metallated GTP Cyclohydrolase Type IB · the same entry in another collection · chain A against A, TM-score 1.00
- Q5F9K6 · AlphaFold monomer V2.0 prediction for GTP cyclohydrolase FOLE2 (Q5F9K6) · 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 Q5F9K6
- Elsewhere: RCSB PDB 3D2O · PDBe 3D2O · UniProt Q5F9K6
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