MolNFT v1 · #189769 · protein
Pseudouridine bound structure of pseudouridine kinase (puki) from escherichia COLI strain B
7VVA: “Pseudouridine bound structure of pseudouridine kinase (puki) from escherichia COLI strain B”. X-ray diffraction, 1 ligand (FJF), 20 pockets (best druggability 0.81). MolNFT v1 #189769 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7VVA
- Type
- protein
- Length
- 2,105 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pseudouridine kinase
- EC
- 2.7.1.83
- UniProt
- A0A1V3W5E1
- Ligands
- FJF
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 8 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pseudouridine kinase (EC 2.7.1.83) | protein | 303 | 36% helix, 22% strand | A0A1V3W5E1 |
| B | Pseudouridine kinase (EC 2.7.1.83) | protein | 299 | 38% helix, 22% strand | A0A1V3W5E1 |
| C | Pseudouridine kinase (EC 2.7.1.83) | protein | 298 | 37% helix, 21% strand | A0A1V3W5E1 |
| D | Pseudouridine kinase (EC 2.7.1.83) | protein | 302 | 36% helix, 22% strand | A0A1V3W5E1 |
| E | Pseudouridine kinase (EC 2.7.1.83) | protein | 300 | 36% helix, 21% strand | A0A1V3W5E1 |
| F | Pseudouridine kinase (EC 2.7.1.83) | protein | 262 | 37% helix, 20% strand | A0A1V3W5E1 |
| G | Pseudouridine kinase (EC 2.7.1.83) | protein | 201 | 29% helix, 21% strand | A0A1V3W5E1 |
| H | Pseudouridine kinase (EC 2.7.1.83) | protein | 140 | 25% helix, 29% strand | A0A1V3W5E1 |
Ligands and binding sites
- FJF · 5-[(2~{S},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-1~{H}-pyrimidine-2,4-dione · ligand · 4 copies · chains A, H, B, G, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 958 | 0.81 | 0.83 | 80 | empty |
| 2 | 877 | 0.76 | 0.79 | 89 | empty |
| 3 | 422 | 0.75 | 0.85 | 62 | FJF |
| 4 | 636 | 0.72 | 0.80 | 56 | FJF |
| 5 | 749 | 0.70 | 0.77 | 71 | empty |
Interfaces
12 interfaces between chains.
- B–G · 1415 Ų buried · 22 hydrogen bonds · protein-protein
- A–H · 1395 Ų buried · 15 hydrogen bonds · protein-protein
- D–F · 1321 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 689 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 646 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7VVA · Pseudouridine bound structure of Pseudouridine kinase (PUKI) from Escherichia coli strain… · 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 A0A1V3W5E1
- Elsewhere: RCSB PDB 7VVA · PDBe 7VVA · UniProt A0A1V3W5E1
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