MolNFT v1 · #139988 · protein
Crystal structure of the complex of 059-152-fv and EGFR-ecd
5XWD · Epidermal growth factor receptor: “Crystal structure of the complex of 059-152-fv and EGFR-ecd”. X-ray diffraction, 4 ligands (NAG, MAN, BMA), 8 pockets (best druggability 0.49). MolNFT v1 #139988 on GenesisL1: 3D structure, binding…
- PDB
- 5XWD
- Type
- protein
- Length
- 838 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epidermal growth factor receptor; Vh chain of 059-152; Vl chain of 059-152
- EC
- 2.7.10.1
- UniProt
- P00533
- Ligands
- NAG, MAN, BMA, ZN
- Pockets
- 8 · best druggability 0.49
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 611 | 14% helix, 26% strand | P00533 |
| H | Vh chain of 059-152 | protein | 119 | 5% helix, 48% strand | — |
| D | Vl chain of 059-152 | protein | 108 | 6% helix, 46% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, H, D
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A, H
- BMA · beta-D-mannopyranose · sugar · chains A
- ZN · Zinc ion · metal · 20 copies · chains A, H, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 150 | 0.49 | 0.78 | 28 | NAG |
| 2 | 123 | 0.42 | 0.76 | 26 | empty |
| 3 | 123 | 0.40 | 0.75 | 21 | empty |
| 4 | 59 | 0.37 | 0.79 | 16 | NAG |
| 5 | 88 | 0.36 | 0.75 | 19 | ZN |
Interfaces
3 interfaces between chains.
- H–D · 861 Ų buried · 8 hydrogen bonds · protein-protein
- A–H · 757 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 547 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 5XWD · Crystal structure of the complex of 059-152-Fv and EGFR-ECD · the same entry in another collection · chain A against A, TM-score 1.00
- P00533 · AlphaFold monomer V2.0 prediction for epidermal growth factor receptor (P00533) · a predicted model of the same protein · chain A against A, TM-score 0.90
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 P00533
- Elsewhere: RCSB PDB 5XWD · PDBe 5XWD · UniProt P00533
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