Research workbench
Crystal structure of a nucleotide sugar transporter with bound nucleotide sugar.
Analyse Crystal structure of a nucleotide sugar transporter with bound nucleotide sugar. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OGK
- Type
- protein
- Length
- 2,359 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GDP-mannose transporter 1
- UniProt
- P40107
- Ligands
- GDD
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GDP-mannose transporter 1 | protein | 292 | 78% helix, 0% strand | P40107 |
| B | GDP-mannose transporter 1 | protein | 297 | 79% helix, 0% strand | P40107 |
| C, D, F, H | GDP-mannose transporter 1 | protein | 294 | 78% helix, 0% strand | P40107 |
| E | GDP-mannose transporter 1 | protein | 298 | 79% helix, 0% strand | P40107 |
| G | GDP-mannose transporter 1 | protein | 296 | 77% helix, 0% strand | P40107 |
Ligands and binding sites
- GDD · Guanosine-5'-diphosphate-alpha-D-mannose · ligand · 3 copies · chains A, D, E
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 8 copies · chains A, B, C, E, D, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1038 | 0.81 | 0.82 | 75 | empty |
| 2 | 1167 | 0.79 | 0.80 | 76 | empty |
| 3 | 1114 | 0.79 | 0.80 | 75 | empty |
| 4 | 1164 | 0.78 | 0.80 | 68 | empty |
| 5 | 1138 | 0.78 | 0.80 | 78 | GDD |
Interfaces
10 interfaces between chains.
- C–E · 562 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 551 Ų buried · 2 hydrogen bonds · protein-protein
- B–F · 306 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 305 Ų buried · 8 hydrogen bonds · protein-protein
- F–G · 293 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5OGK · Crystal structure of a nucleotide sugar transporter with bound nucleotide sugar. · the same entry in another collection · chain H against H, TM-score 1.00
- P40107 · AlphaFold monomer V2.0 prediction for GDP-mannose transporter 1 (P40107) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P40107
- Elsewhere: RCSB PDB 5OGK · PDBe 5OGK · UniProt P40107
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