MolNFT v1 · #115537 · protein
Structural insights into the mechanism of escherichia COLI ymdb
5CMS · O-acetyl-ADP-ribose deacetylase: “Structural insights into the mechanism of escherichia COLI ymdb”. X-ray diffraction, 2 ligands (APR, SO4), 20 pockets (best druggability 0.80). MolNFT v1 #115537 on GenesisL1: 3D structure, binding…
- PDB
- 5CMS
- Type
- protein
- Length
- 3,097 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
- C3TEL7
- Ligands
- APR, SO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R, F, H, J, M, O, P | O-acetyl-ADP-ribose deacetylase (EC 3.5.1.-) | protein | 172 | 42% helix, 18% strand | C3TEL7 |
| A, B, C, D, E, Q | O-acetyl-ADP-ribose deacetylase (EC 3.5.1.-) | protein | 173 | 43% helix, 18% strand | C3TEL7 |
| G, I, K, L, N | O-acetyl-ADP-ribose deacetylase (EC 3.5.1.-) | protein | 171 | 43% helix, 18% strand | C3TEL7 |
Ligands and binding sites
- APR · Adenosine-5-diphosphoribose · ligand · 18 copies · chains R, A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q
- 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 893 | 0.80 | 0.82 | 101 | APR |
| 2 | 1043 | 0.78 | 0.80 | 105 | APR, SO4 |
| 3 | 1129 | 0.78 | 0.80 | 106 | APR |
| 4 | 1076 | 0.78 | 0.80 | 112 | APR |
| 5 | 1147 | 0.78 | 0.80 | 111 | APR |
Interfaces
32 interfaces between chains.
- C–N · 596 Ų buried · 14 hydrogen bonds · protein-protein
- D–I · 594 Ų buried · 12 hydrogen bonds · protein-protein
- M–P · 585 Ų buried · 12 hydrogen bonds · protein-protein
- G–Q · 578 Ų buried · 13 hydrogen bonds · protein-protein
- A–L · 575 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
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 C3TEL7
- Elsewhere: RCSB PDB 5CMS · PDBe 5CMS · UniProt C3TEL7
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