MolNFT v1 · #119653 · protein
BT1596 in complex with its substrate 4,5 unsaturated uronic acid alpha 1,4 D-glucosamine-2-N, 6-O-disulfate
5G2T · 2-O glycosaminoglycan sulfatase: “BT1596 in complex with its substrate 4,5 unsaturated uronic acid alpha 1,4 D-glucosamine-2-N, 6-O-disulfate”. X-ray diffraction, 4 ligands (UAP, SGN, ZN), 18 pockets (best druggability 0.77). MolNFT…
- PDB
- 5G2T
- Type
- protein
- Length
- 1,861 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-O glycosaminoglycan sulfatase
- EC
- 3.1.6.18
- UniProt
- Q8A7C8
- Ligands
- UAP, SGN, ZN, CL
- Pockets
- 18 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-O glycosaminoglycan sulfatase (EC 3.1.6.18) | protein | 467 | 36% helix, 15% strand | Q8A7C8 |
| B | 2-O glycosaminoglycan sulfatase (EC 3.1.6.18) | protein | 465 | 35% helix, 15% strand | Q8A7C8 |
| C | 2-O glycosaminoglycan sulfatase (EC 3.1.6.18) | protein | 465 | 36% helix, 15% strand | Q8A7C8 |
| D | 2-O glycosaminoglycan sulfatase (EC 3.1.6.18) | protein | 464 | 36% helix, 15% strand | Q8A7C8 |
Ligands and binding sites
- UAP · 4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid · ligand · 4 copies · chains A, B, C, D
- SGN · 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · sugar · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 33 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 773 | 0.77 | 0.81 | 92 | EDO, UAP, CL |
| 2 | 1092 | 0.75 | 0.78 | 110 | empty |
| 3 | 1085 | 0.75 | 0.78 | 113 | SGN, UAP, EDO, CL |
| 4 | 205 | 0.54 | 0.78 | 32 | EDO |
| 5 | 216 | 0.52 | 0.77 | 24 | EDO |
Interfaces
5 interfaces between chains.
- B–C · 525 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 427 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 298 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 156 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 113 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5G2T · BT1596 in complex with its substrate 4,5 unsaturated uronic acid alpha 1,4… · the same entry in another collection · chain D against D, TM-score 1.00
- Q8A7C8 · AlphaFold monomer V2.0 prediction for delta 4,5-hexuronate-2-O-sulfatase (Q8A7C8) · a predicted model of the same protein · chain D 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 Q8A7C8
- Elsewhere: RCSB PDB 5G2T · PDBe 5G2T · UniProt Q8A7C8
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