Research workbench
Structure of vcindy in complex with terephthalate
Analyse Structure of vcindy in complex with terephthalate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WTX
- Type
- protein
- Length
- 1,780 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dass family sodium-coupled anion symporter
- UniProt
- A0A0H3AG83
- Ligands
- UB7, NA
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D, A, B | Dass family sodium-coupled anion symporter | protein | 445 | 73% helix, 0% strand | A0A0H3AG83 |
Ligands and binding sites
- UB7 · terephthalic acid · ligand · 4 copies · chains C, D, A, B
- NA · Sodium ion · metal · 8 copies · chains C, D, 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 114 | 0.81 | 0.99 | 16 | empty |
| 2 | 105 | 0.80 | 0.98 | 16 | empty |
| 3 | 788 | 0.76 | 0.80 | 90 | UB7 |
| 4 | 54 | 0.69 | 0.96 | 12 | empty |
| 5 | 292 | 0.67 | 0.82 | 40 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2124 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 2116 Ų buried · 14 hydrogen bonds · protein-protein
- D–B · 287 Ų buried · 1 hydrogen bond · protein-protein
- C–B · 54 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 6WTX · Structure of VcINDY in complex with terephthalate · 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 A0A0H3AG83
- Elsewhere: RCSB PDB 6WTX · PDBe 6WTX · UniProt A0A0H3AG83
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