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Crystal structure of the single-chain fv (scfv) fragment of an anti- ERBB2 antibody CHA21 in complex with residues 1-192 of ERBB2 extracellular domain
Analyse Crystal structure of the single-chain fv (scfv) fragment of an anti- ERBB2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3H3B
- Type
- protein
- Length
- 852 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor tyrosine-protein kinase erbb-2; Anti-ERBB2 antibody CHA21
- EC
- 2.7.10.1
- UniProt
- P04626
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor tyrosine-protein kinase erbb-2 (EC 2.7.10.1) | protein | 193 | 10% helix, 24% strand | P04626 |
| B | Receptor tyrosine-protein kinase erbb-2 (EC 2.7.10.1) | protein | 189 | 13% helix, 24% strand | P04626 |
| C | Anti-ERBB2 antibody CHA21 | protein | 234 | 6% helix, 50% strand | — |
| D | Anti-ERBB2 antibody CHA21 | protein | 236 | 4% helix, 50% strand | — |
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 998 | 0.82 | 0.83 | 129 | empty |
| 2 | 357 | 0.61 | 0.78 | 48 | empty |
| 3 | 59 | 0.39 | 0.80 | 16 | empty |
| 4 | 84 | 0.37 | 0.76 | 24 | empty |
| 5 | 78 | 0.34 | 0.75 | 22 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1003 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 973 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 501 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 489 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 398 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 3H3B · Crystal structure of the single-chain Fv (scFv) fragment of an anti-ErbB2 antibody chA21… · the same entry in another collection · chain A against A, TM-score 1.00
- P04626 · AlphaFold monomer V2.0 prediction for receptor tyrosine-protein kinase erbb-2 (P04626) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 P04626
- Elsewhere: RCSB PDB 3H3B · PDBe 3H3B · UniProt P04626
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