Research workbench
Apo form of UIC2 Fab complex of human-mouse chimeric ABCB1 (ABCB1HM)
Analyse Apo form of UIC2 Fab complex of human-mouse chimeric ABCB1 (ABCB1HM) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FN4
- Type
- protein
- Length
- 1,626 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Apo form of human-mouse chimeric ABCB1 (ABCB1HM) in complex with antigen binding fragment…
- Ligands
- 3PE, NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Apo form of human-mouse chimeric ABCB1 (ABCB1HM) in complex with antigen binding fragment of UIC2. | protein | 1181 | 60% helix, 10% strand | — |
| B | UIC2 antigen binding fragment light chain | protein | 220 | 5% helix, 44% strand | — |
| C | UIC2 antigen binding fragment heavy chain | protein | 225 | 3% helix, 45% strand | — |
Ligands and binding sites
- 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · 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 | 850 | 0.87 | 0.89 | 120 | empty |
| 2 | 407 | 0.81 | 0.89 | 57 | empty |
| 3 | 1154 | 0.77 | 0.79 | 104 | empty |
| 4 | 73 | 0.63 | 0.91 | 16 | empty |
| 5 | 58 | 0.58 | 0.90 | 22 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2122 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 935 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 258 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6FN4 · Apo form of UIC2 Fab complex of human-mouse chimeric ABCB1 (ABCB1HM) · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 6FN4 · PDBe 6FN4
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