MolNFT v1 · #33218 · protein
Structure of a CBM6 in complex with neoagarohexaose
2CDP · Beta-agarase 1: “Structure of a CBM6 in complex with neoagarohexaose”. X-ray diffraction, 4 ligands (AAL, GAL, CA), 2 pockets (best druggability 0.70). MolNFT v1 #33218 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2CDP
- Type
- protein
- Length
- 523 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-agarase 1
- UniProt
- Q6DN99
- Ligands
- AAL, GAL, CA, CL
- Pockets
- 2 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 2% helix, 65% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-agarase 1 | protein | 138 | 2% helix, 59% strand | Q6DN99 |
| B | Beta-agarase 1 | protein | 128 | 2% helix, 69% strand | Q6DN99 |
| C | Beta-agarase 1 | protein | 127 | 0% helix, 65% strand | Q6DN99 |
| D | Beta-agarase 1 | protein | 130 | 2% helix, 68% strand | Q6DN99 |
Ligands and binding sites
- AAL · 3,6-anhydro-alpha-L-galactopyranose · ligand · 12 copies · chains A, D, B, C
- GAL · beta-D-galactopyranose · sugar · 12 copies · chains A, D, B, C
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
- CL · Chloride ion · ion · 9 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 829 | 0.70 | 0.76 | 91 | AAL, GAL, EDO, CL |
| 2 | 261 | 0.60 | 0.79 | 36 | CL |
Interfaces
4 interfaces between chains.
- A–B · 286 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 246 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 231 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 59 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2CDP · Structure of a CBM6 in complex with neoagarohexaose · 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 Q6DN99
- Elsewhere: RCSB PDB 2CDP · PDBe 2CDP · UniProt Q6DN99
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