Research workbench
Nanodisc reconstituted human ABCB4 in complex with 4B1-Fab and QA2-Fab (phosphatidylcholine-bound, occluded conformation)
Analyse Nanodisc reconstituted human ABCB4 in complex with 4B1-Fab and QA2-Fab… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NIV
- Type
- protein
- Length
- 2,020 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- QA2 Fab-fragment light chain; Isoform 2 of phosphatidylcholine translocator ABCB4; 4B1…
- EC
- 7.6.2.1
- UniProt
- P21439
- Ligands
- CLR, DLP
- Pockets
- 20 · best druggability 0.90
Structure
electron microscopy · 5 distinct chains · 32% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | QA2 Fab-fragment light chain | protein | 208 | 4% helix, 40% strand | — |
| E | QA2 Fab-fragment light chain | protein | 229 | 3% helix, 29% strand | — |
| A | Isoform 2 of phosphatidylcholine translocator ABCB4 (EC 7.6.2.1) | protein | 1138 | 55% helix, 6% strand | P21439 |
| B | 4B1 Fab-fragment light chain | protein | 211 | 2% helix, 45% strand | — |
| C | 4B1 Fab-fragment light chain | protein | 234 | 4% helix, 43% strand | — |
Ligands and binding sites
- CLR · Cholesterol · ligand · 7 copies · 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 916 | 0.90 | 0.93 | 113 | DLP |
| 2 | 69 | 0.73 | 0.96 | 23 | empty |
| 3 | 561 | 0.71 | 0.80 | 66 | empty |
| 4 | 76 | 0.71 | 0.96 | 25 | empty |
| 5 | 80 | 0.68 | 0.93 | 29 | empty |
Interfaces
5 interfaces between chains.
- D–E · 1917 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1903 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 714 Ų buried · 4 hydrogen bonds · protein-protein
- E–A · 640 Ų buried · 5 hydrogen bonds · protein-protein
- D–A · 230 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7NIV · Nanodisc reconstituted human ABCB4 in complex with 4B1-Fab and QA2-Fab… · the same entry in another collection · chain D against D, 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 0.85
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 7NIV · PDBe 7NIV · UniProt P21439
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