MolNFT v1 · #141431 · protein
Crystal structure analysis of the hppk-dhps in complex with substrates
5Z79 · Hydroxymethyldihydropterin pyrophosphokinase…: “Crystal structure analysis of the hppk-dhps in complex with substrates”. X-ray diffraction, 6 ligands (HH2, PAB, PE0), 20 pockets (best druggability 0.76). MolNFT v1 #141431 on…
- PDB
- 5Z79
- Type
- protein
- Length
- 3,476 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydroxymethyldihydropterin pyrophosphokinase- dihydropteroate synthase, putative
- EC
- 2.5.1.15, 2.7.6.3
- UniProt
- A0A1K9YMY7
- Ligands
- HH2, PAB, PE0, APC, 5AD, MG
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 6 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hydroxymethyldihydropterin pyrophosphokinase- dihydropteroate synthase, putative (EC 2.5.1.15, 2.7.6.3) | protein | 588 | 42% helix, 16% strand | A0A1K9YMY7 |
| B | Hydroxymethyldihydropterin pyrophosphokinase- dihydropteroate synthase, putative (EC 2.5.1.15, 2.7.6.3) | protein | 562 | 42% helix, 16% strand | A0A1K9YMY7 |
| C | Hydroxymethyldihydropterin pyrophosphokinase- dihydropteroate synthase, putative (EC 2.5.1.15, 2.7.6.3) | protein | 599 | 43% helix, 16% strand | A0A1K9YMY7 |
| D | Hydroxymethyldihydropterin pyrophosphokinase- dihydropteroate synthase, putative (EC 2.5.1.15, 2.7.6.3) | protein | 577 | 43% helix, 17% strand | A0A1K9YMY7 |
| E | Hydroxymethyldihydropterin pyrophosphokinase- dihydropteroate synthase, putative (EC 2.5.1.15, 2.7.6.3) | protein | 584 | 43% helix, 16% strand | A0A1K9YMY7 |
| F | Hydroxymethyldihydropterin pyrophosphokinase- dihydropteroate synthase, putative (EC 2.5.1.15, 2.7.6.3) | protein | 566 | 43% helix, 17% strand | A0A1K9YMY7 |
Ligands and binding sites
- HH2 · 6-hydroxymethylpterin-diphosphate · ligand · 6 copies · chains A, B, C, D, E, F
- PAB · 4-aminobenzoic acid · ligand · 6 copies · chains A, B, C, D, E, F
- PE0 · Pterine · ligand · 4 copies · chains A, C, D, E
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · 2 copies · chains A, C
- 5AD · 5'-deoxyadenosine · ligand · 2 copies · chains B, D
- MG · Magnesium ion · metal · 4 copies · chains A, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 183 | 0.76 | 0.92 | 35 | HH2, PAB |
| 2 | 181 | 0.76 | 0.92 | 33 | HH2, PAB, MG |
| 3 | 180 | 0.75 | 0.91 | 37 | HH2, PAB |
| 4 | 208 | 0.73 | 0.89 | 43 | HH2, PAB, MG |
| 5 | 321 | 0.73 | 0.85 | 54 | HH2, PAB, MG |
Interfaces
6 interfaces between chains.
- C–D · 1652 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 1638 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 1636 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 168 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 151 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5Z79 · Crystal Structure Analysis of the HPPK-DHPS in complex with substrates · 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 A0A1K9YMY7
- Elsewhere: RCSB PDB 5Z79 · PDBe 5Z79 · UniProt A0A1K9YMY7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.