MolNFT v1 · #25032 · protein
Crystal structure of purine phosphoribosyltransferase from pyrococcus horikoshii OT3
1VDM: “Crystal structure of purine phosphoribosyltransferase from pyrococcus horikoshii OT3”. X-ray diffraction, 20 pockets (best druggability 0.89). MolNFT v1 #25032 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1VDM
- Type
- protein
- Length
- 1,778 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purine phosphoribosyltransferase
- EC
- 2.4.2.-
- UniProt
- O57827
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 11 distinct chains · 26% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Purine phosphoribosyltransferase (EC 2.4.2.-) | protein | 151 | 26% helix, 32% strand | O57827 |
| B, L | Purine phosphoribosyltransferase (EC 2.4.2.-) | protein | 149 | 26% helix, 36% strand | O57827 |
| C | Purine phosphoribosyltransferase (EC 2.4.2.-) | protein | 143 | 25% helix, 31% strand | O57827 |
| D | Purine phosphoribosyltransferase (EC 2.4.2.-) | protein | 147 | 27% helix, 35% strand | O57827 |
| E | Purine phosphoribosyltransferase (EC 2.4.2.-) | protein | 149 | 26% helix, 34% strand | O57827 |
| F | Purine phosphoribosyltransferase (EC 2.4.2.-) | protein | 150 | 25% helix, 36% strand | O57827 |
| G | Purine phosphoribosyltransferase (EC 2.4.2.-) | protein | 152 | 24% helix, 34% strand | O57827 |
| H | Purine phosphoribosyltransferase (EC 2.4.2.-) | protein | 149 | 25% helix, 37% strand | O57827 |
| I | Purine phosphoribosyltransferase (EC 2.4.2.-) | protein | 146 | 27% helix, 32% strand | O57827 |
| J | Purine phosphoribosyltransferase (EC 2.4.2.-) | protein | 147 | 27% helix, 35% strand | O57827 |
| K | Purine phosphoribosyltransferase (EC 2.4.2.-) | protein | 146 | 27% helix, 34% strand | O57827 |
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1043 | 0.89 | 0.91 | 81 | empty |
| 2 | 808 | 0.87 | 0.89 | 50 | empty |
| 3 | 810 | 0.86 | 0.89 | 49 | empty |
| 4 | 1091 | 0.74 | 0.76 | 72 | empty |
| 5 | 1188 | 0.73 | 0.76 | 84 | empty |
Interfaces
33 interfaces between chains.
- G–H · 1100 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 1098 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 1081 Ų buried · 11 hydrogen bonds · protein-protein
- K–L · 1058 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1051 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 1VDM · Crystal structure of purine phosphoribosyltransferase from Pyrococcus horikoshii Ot3 · 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 O57827
- Elsewhere: RCSB PDB 1VDM · PDBe 1VDM · UniProt O57827
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.