MolNFT v1 · #33217 · protein
Structure of agarase carbohydrate binding module in complex with neoagarohexaose
2CDO · Beta-agarase 1: “Structure of agarase carbohydrate binding module in complex with neoagarohexaose”. X-ray diffraction, 4 ligands (AAL, GAL, CA), 2 pockets (best druggability 0.72). MolNFT v1 #33217 on GenesisL1: 3D structure…
- PDB
- 2CDO
- Type
- protein
- Length
- 548 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 0.72
Structure
x-ray diffraction · 3 distinct chains · 1% helix, 60% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-agarase 1 | protein | 138 | 2% helix, 58% strand | Q6DN99 |
| B, D | Beta-agarase 1 | protein | 137 | 2% helix, 60% strand | Q6DN99 |
| C | Beta-agarase 1 | protein | 136 | 0% helix, 62% strand | Q6DN99 |
Ligands and binding sites
- AAL · 3,6-anhydro-alpha-L-galactopyranose · ligand · 12 copies · chains A, D, C, B
- GAL · beta-D-galactopyranose · sugar · 12 copies · chains A, D, C, B
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
- CL · Chloride ion · ion · 10 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B, D, C
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 | 1018 | 0.72 | 0.76 | 108 | AAL, GAL, EDO, CL |
| 2 | 261 | 0.61 | 0.80 | 37 | CL |
Interfaces
4 interfaces between chains.
- A–B · 284 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 263 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 245 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 67 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 2CDO · structure of agarase carbohydrate binding module 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 2CDO · PDBe 2CDO · UniProt Q6DN99
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