MolNFT v1 · #156847 · protein
Structure of herceptin Fab without antigen
6MH2 · Herceptin Fab arm light chain: “Structure of herceptin Fab without antigen”. X-ray diffraction, 7 pockets (best druggability 0.68). MolNFT v1 #156847 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6MH2
- Type
- protein
- Length
- 821 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Herceptin Fab arm light chain; Herceptin Fab arm heavy chain
- UniProt
- Q7Z3Y4
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Herceptin Fab arm light chain | protein | 214 | 6% helix, 50% strand | Q7Z3Y4 |
| B | Herceptin Fab arm heavy chain | protein | 208 | 7% helix, 53% strand | — |
| C | Herceptin Fab arm light chain | protein | 197 | 4% helix, 50% strand | Q7Z3Y4 |
| D | Herceptin Fab arm heavy chain | protein | 202 | 7% helix, 51% strand | — |
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 132 | 0.68 | 0.89 | 25 | empty |
| 2 | 305 | 0.57 | 0.77 | 47 | empty |
| 3 | 349 | 0.53 | 0.73 | 43 | empty |
| 4 | 200 | 0.51 | 0.77 | 26 | empty |
| 5 | 240 | 0.48 | 0.74 | 38 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1580 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1338 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 644 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6MH2 · Structure of Herceptin Fab without antigen · 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
- Every structure of UniProt Q7Z3Y4
- Elsewhere: RCSB PDB 6MH2 · PDBe 6MH2 · UniProt Q7Z3Y4
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