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
- 6THJ
- Type
- protein
- Length
- 1,662 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PLYP35
- UniProt
- A8ATR6
- Ligands
- NAG
- Pockets
- 10 · best druggability 0.57
Structure
x-ray diffraction · 4 distinct chains · 4% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, F, G, J | PLYP35 | protein | 139 | 4% helix, 56% strand | A8ATR6 |
| B | PLYP35 | protein | 137 | 4% helix, 55% strand | A8ATR6 |
| H | PLYP35 | protein | 138 | 4% helix, 55% strand | A8ATR6 |
| I, K, L | PLYP35 | protein | 138 | 4% helix, 56% strand | A8ATR6 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 21 copies · chains A, B, C, K, D, I, E, F, G, H, J, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 221 | 0.57 | 0.79 | 32 | NAG |
| 2 | 52 | 0.56 | 0.90 | 18 | empty |
| 3 | 249 | 0.56 | 0.77 | 42 | NAG |
| 4 | 183 | 0.55 | 0.79 | 29 | NAG |
| 5 | 197 | 0.54 | 0.78 | 29 | NAG |
Interfaces
12 interfaces between chains.
- C–J · 934 Ų buried · 5 hydrogen bonds · protein-protein
- D–G · 926 Ų buried · 7 hydrogen bonds · protein-protein
- B–H · 910 Ų buried · 6 hydrogen bonds · protein-protein
- K–L · 880 Ų buried · 10 hydrogen bonds · protein-protein
- F–H · 628 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6THJ · 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 6THJ · PDBe 6THJ · UniProt A8ATR6
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