Research workbench
CBDP35 native structure
Analyse CBDP35 native structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6S4S
- Type
- protein
- Length
- 1,667 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PLYP35
- UniProt
- A8ATR6
- Pockets
- 11 · best druggability 0.58
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PLYP35 | protein | 140 | 4% helix, 56% strand | A8ATR6 |
| B, D, E, F, G, H, I, L, K | PLYP35 | protein | 139 | 6% helix, 57% strand | A8ATR6 |
| C | PLYP35 | protein | 139 | 4% helix, 55% strand | A8ATR6 |
| J | PLYP35 | protein | 137 | 4% helix, 55% strand | A8ATR6 |
Ligands and binding sites
- MLI · Malonate ion · additive · 5 copies · chains B, C, D, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 228 | 0.58 | 0.79 | 28 | empty |
| 2 | 223 | 0.57 | 0.79 | 30 | MLI |
| 3 | 205 | 0.56 | 0.79 | 30 | MLI |
| 4 | 242 | 0.56 | 0.78 | 36 | empty |
| 5 | 216 | 0.56 | 0.79 | 29 | MLI |
Interfaces
13 interfaces between chains.
- A–H · 986 Ų buried · 6 hydrogen bonds · protein-protein
- C–J · 954 Ų buried · 6 hydrogen bonds · protein-protein
- B–K · 933 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 900 Ų buried · 3 hydrogen bonds · protein-protein
- F–G · 559 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6S4S · CBDP35 Native structure · 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 A8ATR6
- Elsewhere: RCSB PDB 6S4S · PDBe 6S4S · UniProt A8ATR6
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