MolNFT v1 · #164578 · protein
Glycoside hydrolase family 109 from akkermansia muciniphila in complex with galnac and NAD+.
6T2B · Glycosyl hydrolase family 109 protein 2: “Glycoside hydrolase family 109 from akkermansia muciniphila in complex with galnac and NAD+.”. X-ray diffraction, 2 ligands (NAD, A2G), 16 pockets (best druggability 0.78). MolNFT v1 #164578…
- PDB
- 6T2B
- Type
- protein
- Length
- 1,750 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyl hydrolase family 109 protein 2
- UniProt
- A0A2N8I799
- Ligands
- NAD, A2G
- Pockets
- 16 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycosyl hydrolase family 109 protein 2 | protein | 438 | 41% helix, 18% strand | A0A2N8I799 |
| B | Glycosyl hydrolase family 109 protein 2 | protein | 439 | 41% helix, 18% strand | A0A2N8I799 |
| C | Glycosyl hydrolase family 109 protein 2 | protein | 436 | 41% helix, 18% strand | A0A2N8I799 |
| D | Glycosyl hydrolase family 109 protein 2 | protein | 437 | 41% helix, 18% strand | A0A2N8I799 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 4 copies · chains A, B, C, D
- PGE · Triethylene glycol · additive · chains A, C
- 1PE · Pentaethylene glycol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 306 | 0.78 | 0.90 | 41 | empty |
| 2 | 395 | 0.75 | 0.85 | 52 | empty |
| 3 | 392 | 0.65 | 0.79 | 50 | A2G, NAD |
| 4 | 351 | 0.63 | 0.79 | 46 | A2G, NAD |
| 5 | 325 | 0.63 | 0.79 | 46 | A2G, NAD |
Interfaces
3 interfaces between chains.
- A–C · 1770 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 1759 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 130 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6T2B · Glycoside hydrolase family 109 from Akkermansia muciniphila in complex with GalNAc and… · the same entry in another collection · chain C against C, 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 A0A2N8I799
- Elsewhere: RCSB PDB 6T2B · PDBe 6T2B · UniProt A0A2N8I799
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