MolNFT v1 · #137290 · protein
Crystal structure of dutp pyrophosphatase protein, from naegleria fowleri
5VJY: “Crystal structure of dutp pyrophosphatase protein, from naegleria fowleri”. X-ray diffraction, 6 pockets (best druggability 0.78). MolNFT v1 #137290 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5VJY
- Type
- protein
- Length
- 658 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dutp pyrophosphatase
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Dutp pyrophosphatase | protein | 131 | 5% helix, 41% strand | — |
| B, C, E | Dutp pyrophosphatase | protein | 132 | 5% helix, 47% strand | — |
Ligands and binding sites
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · 5 copies · chains A, B, D, C, E
- EDO · 1,2-ethanediol · additive · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 125 | 0.78 | 0.97 | 26 | empty |
| 2 | 217 | 0.59 | 0.80 | 40 | BTB, EDO |
| 3 | 304 | 0.55 | 0.76 | 44 | BTB |
| 4 | 162 | 0.48 | 0.77 | 27 | BTB |
| 5 | 99 | 0.41 | 0.77 | 21 | BTB |
Interfaces
6 interfaces between chains.
- B–C · 1667 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 1658 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1648 Ų buried · 24 hydrogen bonds · protein-protein
- C–E · 488 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 451 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5VJY · Crystal Structure of dUTP pyrophosphatase protein, from Naegleria fowleri · 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
- Elsewhere: RCSB PDB 5VJY · PDBe 5VJY
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