Research workbench
Cdtb double heptamer short form modeled from cryo-EM MAP reconstructed using C1 symmetry
Analyse Cdtb double heptamer short form modeled from cryo-EM MAP reconstructed using C1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6O2O
- Type
- protein
- Length
- 9,218 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribosyltransferase binding component
- UniProt
- A8DS70
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 3 distinct chains · 9% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, F, H, J, L | ADP-ribosyltransferase binding component | protein | 659 | 8% helix, 37% strand | A8DS70 |
| C, E, G, I, K, M | ADP-ribosyltransferase binding component | protein | 658 | 9% helix, 29% strand | A8DS70 |
| Z | ADP-ribosyltransferase binding component | protein | 657 | 9% helix, 28% strand | A8DS70 |
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 | 1102 | 0.88 | 0.90 | 146 | empty |
| 2 | 997 | 0.87 | 0.88 | 114 | empty |
| 3 | 876 | 0.84 | 0.86 | 84 | empty |
| 4 | 893 | 0.84 | 0.86 | 102 | empty |
| 5 | 988 | 0.84 | 0.85 | 106 | empty |
Interfaces
35 interfaces between chains.
- J–L · 4136 Ų buried · 77 hydrogen bonds · protein-protein
- A–B · 4104 Ų buried · 75 hydrogen bonds · protein-protein
- A–L · 4103 Ų buried · 65 hydrogen bonds · protein-protein
- H–J · 3991 Ų buried · 76 hydrogen bonds · protein-protein
- F–H · 3983 Ų buried · 74 hydrogen bonds · protein-protein
Compared structures
- 6O2O · CDTb Double Heptamer Short Form Modeled from Cryo-EM Map Reconstructed using C1 Symmetry · 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 A8DS70
- Elsewhere: RCSB PDB 6O2O · PDBe 6O2O · UniProt A8DS70
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