MolNFT v1 · #163403 · protein
Metabolism of multiple glycosaminoglycans by bacteroides thetaiotaomicron is orchestrated by a versatile core genetic locus (BT33494S-sulf)
6S21 · Endo-4-O-sulfatase: “Metabolism of multiple glycosaminoglycans by bacteroides thetaiotaomicron is orchestrated by a versatile core…”. X-ray diffraction, 4 ligands (ASG, GCD, BDP), 8 pockets (best druggability 0.72). MolNFT v1…
- PDB
- 6S21
- Type
- protein
- Length
- 1,457 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-4-O-sulfatase
- EC
- 3.1.6.-
- UniProt
- Q8A2F6
- Ligands
- ASG, GCD, BDP, CA
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Endo-4-O-sulfatase (EC 3.1.6.-) | protein | 486 | 29% helix, 17% strand | Q8A2F6 |
| B | Endo-4-O-sulfatase (EC 3.1.6.-) | protein | 485 | 29% helix, 18% strand | Q8A2F6 |
Ligands and binding sites
- ASG · 2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose · ligand · 3 copies · chains A, B, C
- GCD · 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid · ligand · 3 copies · chains A, B, C
- BDP · beta-D-glucopyranuronic acid · sugar · 3 copies · chains A, B, C
- CA · Calcium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1152 | 0.72 | 0.76 | 101 | BDP, ASG |
| 2 | 151 | 0.63 | 0.86 | 28 | empty |
| 3 | 128 | 0.61 | 0.86 | 27 | empty |
| 4 | 139 | 0.61 | 0.85 | 27 | empty |
| 5 | 350 | 0.55 | 0.75 | 30 | empty |
Interfaces
2 interfaces between chains.
- A–B · 427 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 215 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6S21 · Metabolism of multiple glycosaminoglycans by bacteroides thetaiotaomicron is orchestrated… · the same entry in another collection · chain C against C, TM-score 1.00
- Q8A2F6 · AlphaFold monomer V2.0 prediction for endo-4-O-sulfatase (Q8A2F6) · a predicted model of the same protein · 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 Q8A2F6
- Elsewhere: RCSB PDB 6S21 · PDBe 6S21 · UniProt Q8A2F6
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