MolNFT v1 · #162511 · protein
Mucin 2 D3 domain
6RBF · Mucin-2: “Mucin 2 D3 domain”. X-ray diffraction, 3 ligands (NAG, CA, SO4), 20 pockets (best druggability 0.81). MolNFT v1 #162511 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6RBF
- Type
- protein
- Length
- 1,418 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mucin-2
- UniProt
- Q02817
- Ligands
- NAG, CA, SO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mucin-2 | protein | 372 | 22% helix, 27% strand | Q02817 |
| B | Mucin-2 | protein | 364 | 22% helix, 30% strand | Q02817 |
| C | Mucin-2 | protein | 341 | 21% helix, 28% strand | Q02817 |
| D | Mucin-2 | protein | 341 | 24% helix, 28% strand | Q02817 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 6 copies · chains B, C, D
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 658 | 0.81 | 0.85 | 89 | GOL |
| 2 | 890 | 0.80 | 0.82 | 104 | empty |
| 3 | 304 | 0.63 | 0.80 | 40 | empty |
| 4 | 229 | 0.60 | 0.81 | 34 | empty |
| 5 | 185 | 0.57 | 0.81 | 25 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1193 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 1177 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 216 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 198 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 113 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 61 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6RBF · Mucin 2 D3 domain · 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 Q02817
- Elsewhere: RCSB PDB 6RBF · PDBe 6RBF · UniProt Q02817
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