MolNFT v1 · #65986 · protein
Crystal structure of E. COLI HPPK(N10A) in complex with mgampcpp
3HD1 · 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine…: “Crystal structure of E. COLI HPPK(N10A) in complex with mgampcpp”. X-ray diffraction, 3 ligands (APC, MG, CL), 2 pockets (best druggability 0.41). MolNFT v1 #65986 on GenesisL1…
- PDB
- 3HD1
- Type
- protein
- Length
- 158 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
- EC
- 2.7.6.3
- UniProt
- P26281
- Ligands
- APC, MG, CL
- Pockets
- 2 · best druggability 0.41
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase (EC 2.7.6.3) | protein | 158 | 30% helix, 30% strand | P26281 |
Ligands and binding sites
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 113 | 0.41 | 0.76 | 29 | ACT |
| 2 | 58 | 0.32 | 0.76 | 13 | empty |
Compared structures
- 3HD1 · Crystal structure of E. coli HPPK(N10A) in complex with MgAMPCPP · the same entry in another collection · chain A against A, TM-score 1.00
- P26281 · 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 0.91
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 P26281
- Elsewhere: RCSB PDB 3HD1 · PDBe 3HD1 · UniProt P26281
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