MolNFT v1 · #118160 · protein
E. COLI 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with ampcpp and inhibitor at 1.82 ångström resolution
5ETL · 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine…: “E. COLI 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with ampcpp and inhibitor at 1.82…”. X-ray diffraction, 3 ligands (ATP, 5RV, CA), 6 pockets (best…
- PDB
- 5ETL
- Type
- protein
- Length
- 626 residues
- Chains
- 4
- 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
- ATP, 5RV, CA
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase (EC 2.7.6.3) | protein | 155 | 30% helix, 28% strand | P26281 |
| B | 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase (EC 2.7.6.3) | protein | 155 | 30% helix, 28% strand | P26281 |
| C | 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase (EC 2.7.6.3) | protein | 156 | 30% helix, 28% strand | P26281 |
| D | 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase (EC 2.7.6.3) | protein | 160 | 29% helix, 27% strand | P26281 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- 5RV · 2-[(2-azanyl-6-oxidanylidene-3,9-dihydropurin-8-yl)sulfanylmethyl]benzenecarbonitrile · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 11 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1103 | 0.79 | 0.81 | 107 | CA, ATP, 5RV |
| 2 | 1017 | 0.71 | 0.75 | 99 | CA, ATP, 5RV |
| 3 | 234 | 0.49 | 0.75 | 35 | empty |
| 4 | 68 | 0.37 | 0.78 | 14 | empty |
| 5 | 77 | 0.33 | 0.75 | 19 | empty |
Interfaces
4 interfaces between chains.
- A–B · 327 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 291 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 274 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 247 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5ETL · E. coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with AMPCPP and… · the same entry in another collection · chain A against A, TM-score 1.00
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 5ETL · PDBe 5ETL · UniProt P26281
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