Research workbench
Crystal structure of anti-ERBB3 Fab ISU104 in complex with human ERBB3 extracellular domain 3
Analyse Crystal structure of anti-ERBB3 Fab ISU104 in complex with human ERBB3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7D85
- Type
- protein
- Length
- 1,247 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor tyrosine-protein kinase erbb-3; Anti-ERBB3 Fab heavy chain; Anti-ERBB3 Fab light…
- EC
- 2.7.10.1
- UniProt
- P21860
- Ligands
- NAG
- Pockets
- 17 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Receptor tyrosine-protein kinase erbb-3 (EC 2.7.10.1) | protein | 193 | 18% helix, 21% strand | P21860 |
| B | Anti-ERBB3 Fab heavy chain | protein | 218 | 7% helix, 50% strand | — |
| C, F | Anti-ERBB3 Fab light chain | protein | 213 | 9% helix, 51% strand | — |
| E | Anti-ERBB3 Fab heavy chain | protein | 217 | 8% helix, 53% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 638 | 0.75 | 0.82 | 72 | empty |
| 2 | 754 | 0.70 | 0.77 | 68 | empty |
| 3 | 370 | 0.69 | 0.82 | 50 | empty |
| 4 | 491 | 0.59 | 0.74 | 56 | empty |
| 5 | 323 | 0.54 | 0.74 | 37 | empty |
Interfaces
9 interfaces between chains.
- B–C · 1748 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 1723 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 759 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 749 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 542 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 7D85 · Crystal structure of anti-ErbB3 Fab ISU104 in complex with human ErbB3 extracellular… · the same entry in another collection · chain F against F, TM-score 1.00
- P21860 · AlphaFold monomer V2.0 prediction for receptor tyrosine-protein kinase erbb-3 (P21860) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 P21860
- Elsewhere: RCSB PDB 7D85 · PDBe 7D85 · UniProt P21860
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