Research workbench
Structural insights into the mechanism of escherichia COLI ymdb
Analyse Structural insights into the mechanism of escherichia COLI ymdb in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CB5
- Type
- protein
- Length
- 3,105 residues
- Chains
- 18
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O-acetyl-ADP-ribose deacetylase
- EC
- 3.5.1.-
- UniProt
- P0A8D6
- Ligands
- APR, ZOD, SO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R, A, C, E, F, G, H, I, M, N, P, Q | O-acetyl-ADP-ribose deacetylase (EC 3.5.1.-) | protein | 173 | 42% helix, 18% strand | P0A8D6 |
| B | O-acetyl-ADP-ribose deacetylase (EC 3.5.1.-) | protein | 172 | 42% helix, 18% strand | P0A8D6 |
| D | O-acetyl-ADP-ribose deacetylase (EC 3.5.1.-) | protein | 170 | 42% helix, 18% strand | P0A8D6 |
| J, K, L | O-acetyl-ADP-ribose deacetylase (EC 3.5.1.-) | protein | 172 | 42% helix, 18% strand | P0A8D6 |
| O | O-acetyl-ADP-ribose deacetylase (EC 3.5.1.-) | protein | 171 | 43% helix, 18% strand | P0A8D6 |
Ligands and binding sites
- APR · Adenosine-5-diphosphoribose · ligand · 16 copies · chains R, A, B, C, D, E, G, H, I, J, K, L, N, O, P, Q
- ZOD · [(2R,3R,4R,5R)-5-[[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-2,4-bis(oxidanyl)oxolan-3-yl] ethanoate · ligand · 2 copies · chains F, M
- SO4 · Sulfate ion · ion · 18 copies · chains R, Q, A, F, B, O, C, P, D, M, E, G, H, I, J, K, L, N
- ACT · Acetate ion · additive · 3 copies · chains B, C, J, E, Q
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1136 | 0.84 | 0.85 | 127 | APR, SO4 |
| 2 | 1152 | 0.83 | 0.84 | 125 | SO4, APR, ACT |
| 3 | 1098 | 0.83 | 0.84 | 126 | SO4, APR, ZOD |
| 4 | 1163 | 0.83 | 0.84 | 141 | APR, ACT, SO4 |
| 5 | 756 | 0.82 | 0.85 | 102 | SO4, ZOD, APR |
Interfaces
32 interfaces between chains.
- D–I · 595 Ų buried · 14 hydrogen bonds · protein-protein
- G–Q · 586 Ų buried · 13 hydrogen bonds · protein-protein
- F–K · 586 Ų buried · 14 hydrogen bonds · protein-protein
- R–E · 583 Ų buried · 14 hydrogen bonds · protein-protein
- B–H · 582 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- P0A8D6 · AlphaFold monomer V2.0 prediction for O-acetyl-ADP-ribose deacetylase (P0A8D6) · a predicted model of the same protein · chain O 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 P0A8D6
- Elsewhere: RCSB PDB 5CB5 · PDBe 5CB5 · UniProt P0A8D6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.