Research workbench
Crystal structure of DRUG:PROTON antiporter-1 (DHA1) family sotb, in the inward open conformation (H115A mutant)
Analyse Crystal structure of DRUG:PROTON antiporter-1 (DHA1) family sotb, in the inward… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KKK
- Type
- protein
- Length
- 1,143 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sugar efflux transporter
- UniProt
- P31122
- Ligands
- BNG
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 85% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Sugar efflux transporter | protein | 381 | 85% helix, 1% strand | P31122 |
Ligands and binding sites
- BNG · nonyl beta-D-glucopyranoside · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1129 | 0.80 | 0.81 | 81 | BNG |
| 2 | 949 | 0.79 | 0.81 | 66 | BNG |
| 3 | 1166 | 0.78 | 0.80 | 78 | BNG |
| 4 | 137 | 0.69 | 0.89 | 23 | empty |
| 5 | 62 | 0.62 | 0.92 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–C · 676 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 524 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 84 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6KKK · Crystal structure of Drug:Proton Antiporter-1 (DHA1) Family SotB, in the inward open… · the same entry in another collection · chain A against A, TM-score 1.00
- P31122 · AlphaFold monomer V2.0 prediction for sugar efflux transporter (P31122) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P31122
- Elsewhere: RCSB PDB 6KKK · PDBe 6KKK · UniProt P31122
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