MolNFT v1 · #2921 · protein
7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase from haemophilus influenzae
1CBK · Protein (7,8-dihydro-6-hydroxymethylpterin…: “7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase from haemophilus influenzae”. X-ray diffraction, 2 ligands (ROI, SO4), 4 pockets (best druggability 0.66). MolNFT v1 #2921 on…
- PDB
- 1CBK
- Type
- protein
- Length
- 320 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (7,8-dihydro-6-hydroxymethylpterin- pyrophosphokinase)
- UniProt
- P43777
- Ligands
- ROI, SO4
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein (7,8-dihydro-6-hydroxymethylpterin- pyrophosphokinase) | protein | 160 | 31% helix, 28% strand | P43777 |
Ligands and binding sites
- ROI · 7,8-dihydro-7,7-dimethyl-6-hydroxypterin · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 287 | 0.66 | 0.82 | 26 | empty |
| 2 | 362 | 0.65 | 0.80 | 38 | SO4, ROI |
| 3 | 304 | 0.65 | 0.81 | 29 | empty |
| 4 | 358 | 0.65 | 0.80 | 40 | SO4, ROI |
Interfaces
1 interface between chains.
- A–B · 972 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 1CBK · 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase from haemophilus influenzae · the same entry in another collection · chain A against A, TM-score 1.00
- P43777 · AlphaFold monomer V2.0 prediction for 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P43777
- Elsewhere: RCSB PDB 1CBK · PDBe 1CBK · UniProt P43777
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