Research workbench
Structure of an ABC transporter: part of the structure that could be built de novo
Analyse Structure of an ABC transporter: part of the structure that could be built de… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NJG
- Type
- protein
- Length
- 1,020 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-binding cassette sub-family G member 2; 5D3-Fab heavy chain; 5D3-Fab light chain
- UniProt
- Q9UNQ0
- Ligands
- NAG
- Pockets
- 8 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ATP-binding cassette sub-family G member 2 | protein | 286 | 71% helix, 0% strand | Q9UNQ0 |
| C, E | 5D3-Fab heavy chain | protein | 118 | 3% helix, 53% strand | — |
| D, F | 5D3-Fab light chain | protein | 106 | 0% helix, 40% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, C, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 311 | 0.84 | 0.94 | 35 | empty |
| 2 | 1140 | 0.79 | 0.81 | 97 | empty |
| 3 | 445 | 0.70 | 0.81 | 60 | empty |
| 4 | 472 | 0.69 | 0.80 | 67 | empty |
| 5 | 61 | 0.33 | 0.77 | 20 | empty |
Interfaces
11 interfaces between chains.
- A–B · 1589 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 873 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 864 Ų buried · 7 hydrogen bonds · protein-protein
- A–F · 486 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 480 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5NJG · Structure of an ABC transporter: part of the structure that could be built de novo · the same entry in another collection · chain F against F, TM-score 1.00
- Q9UNQ0 · AlphaFold monomer V2.0 prediction for broad substrate specificity ATP-binding cassette… · a predicted model of the same protein · chain B against A, TM-score 0.95
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 Q9UNQ0
- Elsewhere: RCSB PDB 5NJG · PDBe 5NJG · UniProt Q9UNQ0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.