MolNFT v1 · #128189 · protein
Structure of an ABC transporter: complete structure
5NJ3 · ATP-binding cassette sub-family G member 2: “Structure of an ABC transporter: complete structure”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.84). MolNFT v1 #128189 on GenesisL1: 3D structure, binding sites…
- PDB
- 5NJ3
- Type
- protein
- Length
- 1,958 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
- 20 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ATP-binding cassette sub-family G member 2 | protein | 561 | 57% helix, 8% strand | Q9UNQ0 |
| C, E | 5D3-Fab heavy chain | protein | 208 | 1% helix, 50% strand | — |
| D, F | 5D3-Fab light chain | protein | 210 | 5% helix, 43% 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
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 308 | 0.84 | 0.94 | 32 | empty |
| 2 | 1156 | 0.81 | 0.83 | 140 | empty |
| 3 | 523 | 0.81 | 0.88 | 89 | empty |
| 4 | 1059 | 0.80 | 0.81 | 89 | empty |
| 5 | 904 | 0.79 | 0.82 | 105 | empty |
Interfaces
11 interfaces between chains.
- A–B · 1763 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1188 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 1179 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
- 5NJ3 · Structure of an ABC transporter: complete structure · 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 0.87
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 5NJ3 · PDBe 5NJ3 · UniProt Q9UNQ0
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