MolNFT v1 · #128903 · protein
HER2 in complex with Fab MF3958
5O4G · Receptor tyrosine-protein kinase erbb-2: “HER2 in complex with Fab MF3958”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 11 pockets (best druggability 0.66). MolNFT v1 #128903 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5O4G
- Type
- protein
- Length
- 960 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor tyrosine-protein kinase erbb-2; MF3958 Fab light chain; MF3958 Fab heavy chain
- EC
- 2.7.10.1
- UniProt
- P04626
- Ligands
- NAG, MAN, BMA
- Pockets
- 11 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Receptor tyrosine-protein kinase erbb-2 (EC 2.7.10.1) | protein | 530 | 11% helix, 25% strand | P04626 |
| A | MF3958 Fab light chain | protein | 214 | 3% helix, 47% strand | — |
| B | MF3958 Fab heavy chain | protein | 216 | 7% helix, 44% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains C
- MAN · alpha-D-mannopyranose · sugar · 3 copies
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 710 | 0.66 | 0.75 | 64 | empty |
| 2 | 460 | 0.65 | 0.77 | 55 | empty |
| 3 | 178 | 0.61 | 0.83 | 26 | empty |
| 4 | 102 | 0.48 | 0.80 | 23 | empty |
| 5 | 137 | 0.45 | 0.77 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1791 Ų buried · 10 hydrogen bonds · protein-protein
- C–B · 688 Ų buried · 15 hydrogen bonds · protein-protein
- C–A · 39 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
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 5O4G · PDBe 5O4G · UniProt P04626
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