MolNFT v1 · #23523 · protein
Crystal structure of ADP-ribosylated ribosomal translocase from saccharomyces cerevisiae
1U2R · Elongation factor 2: “Crystal structure of ADP-ribosylated ribosomal translocase from saccharomyces cerevisiae”. X-ray diffraction, 4 ligands (APR, SO1, GDP), 8 pockets (best druggability 0.72). MolNFT v1 #23523 on GenesisL1: 3D…
- PDB
- 1U2R
- Type
- protein
- Length
- 819 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Elongation factor 2
- UniProt
- P32324
- Ligands
- APR, SO1, GDP, MG
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Elongation factor 2 | protein | 819 | 37% helix, 26% strand | P32324 |
Ligands and binding sites
- APR · Adenosine-5-diphosphoribose · ligand · chains A
- SO1 · [1R-(1.alpha.,3a.beta.,4.beta.,4a.beta.,7.beta.,7a.alpha.,8a.beta.)]8a-[(6-deoxy-4-O-methyl-beta-D-altropyranosyloxy)methyl]-4-formyl-4,4A,5,6,7,7A,8,8A-octahydro-7-methyl-3-(1-methylethyl)-1,4-methano-S-indacene-3A(1H)-carboxylic acid · ligand · chains A
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 684 | 0.72 | 0.79 | 63 | empty |
| 2 | 254 | 0.62 | 0.80 | 35 | SO1 |
| 3 | 216 | 0.51 | 0.76 | 27 | empty |
| 4 | 59 | 0.38 | 0.80 | 13 | empty |
| 5 | 107 | 0.37 | 0.74 | 22 | empty |
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, nonstandard).
Compared structures
- 1U2R · Crystal Structure of ADP-ribosylated Ribosomal Translocase from Saccharomyces cerevisiae · the same entry in another collection · chain A against A, TM-score 1.00
- P32324 · AlphaFold monomer V2.0 prediction for elongation factor 2 (P32324) · a predicted model of the same protein · chain A against A, TM-score 0.64
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 P32324
- Elsewhere: RCSB PDB 1U2R · PDBe 1U2R · UniProt P32324
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