Research workbench
Nanodisc reconstituted human ABCB4 in complex with 4B1-Fab (posaconazole-bound, inward-open conformation)
Analyse Nanodisc reconstituted human ABCB4 in complex with 4B1-Fab (posaconazole-bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NIW
- Type
- protein
- Length
- 1,585 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatidylcholine translocator ABCB4; 4B1 Fab-fragment light chain; 4B1 Fab-fragment…
- EC
- 7.6.2.1
- UniProt
- P21439
- Ligands
- CLR, X2N, DLP
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 3 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphatidylcholine translocator ABCB4 (EC 7.6.2.1) | protein | 1140 | 60% helix, 7% strand | P21439 |
| B | 4B1 Fab-fragment light chain | protein | 211 | 2% helix, 36% strand | — |
| C | 4B1 Fab-fragment heavy chain | protein | 234 | 5% helix, 38% strand | — |
Ligands and binding sites
- CLR · Cholesterol · ligand · 6 copies · chains A
- X2N · Posaconazole · ligand · chains A
- DLP · 1,2-dilinoleoyl-sn-glycero-3-phosphocholine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 747 | 0.85 | 0.88 | 70 | X2N, DLP |
| 2 | 104 | 0.78 | 0.97 | 24 | empty |
| 3 | 104 | 0.69 | 0.92 | 28 | empty |
| 4 | 163 | 0.65 | 0.86 | 34 | X2N |
| 5 | 182 | 0.63 | 0.84 | 30 | empty |
Interfaces
2 interfaces between chains.
- B–C · 2033 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 662 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7NIW · Nanodisc reconstituted human ABCB4 in complex with 4B1-Fab (posaconazole-bound… · the same entry in another collection · chain A against A, TM-score 1.00
- P21439 · AlphaFold monomer V2.0 prediction for phosphatidylcholine translocator ABCB4 (P21439) · a predicted model of the same protein · chain A against A, TM-score 0.88
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 P21439
- Elsewhere: RCSB PDB 7NIW · PDBe 7NIW · UniProt P21439
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