Research workbench
Crystal structure of panitumumab in complex with epidermal growth factor receptor domain 3 mutant S468R.
Analyse Crystal structure of panitumumab in complex with epidermal growth factor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5SX5
- Type
- protein
- Length
- 1,225 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Panitumumab Fab light chain; Panitumumab Fab heavy chain; Epidermal growth factor receptor
- EC
- 2.7.10.1
- UniProt
- P00533
- Ligands
- SO4
- Pockets
- 17 · best druggability 0.60
Structure
x-ray diffraction · 6 distinct chains · 10% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| K | Panitumumab Fab light chain | protein | 213 | 6% helix, 53% strand | — |
| J | Panitumumab Fab heavy chain | protein | 207 | 4% helix, 56% strand | — |
| L | Panitumumab Fab light chain | protein | 212 | 6% helix, 52% strand | — |
| H | Panitumumab Fab heavy chain | protein | 207 | 6% helix, 55% strand | — |
| M | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 194 | 18% helix, 21% strand | P00533 |
| N | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 192 | 20% helix, 21% strand | P00533 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 12 copies · chains K, M, L, N, H
- GOL · Glycerol · additive · 4 copies · chains K, L, H
- EDO · 1,2-ethanediol · additive · 3 copies · chains K, J, H, N
- 1PE · Pentaethylene glycol · additive · 3 copies · chains K, J, L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 563 | 0.60 | 0.73 | 64 | EDO, 1PE |
| 2 | 417 | 0.56 | 0.73 | 51 | 1PE |
| 3 | 52 | 0.48 | 0.86 | 17 | empty |
| 4 | 51 | 0.43 | 0.84 | 18 | empty |
| 5 | 143 | 0.43 | 0.76 | 30 | empty |
Interfaces
7 interfaces between chains.
- K–J · 1709 Ų buried · 13 hydrogen bonds · protein-protein
- L–H · 1689 Ų buried · 15 hydrogen bonds · protein-protein
- J–M · 650 Ų buried · 15 hydrogen bonds · protein-protein
- H–N · 644 Ų buried · 16 hydrogen bonds · protein-protein
- K–M · 395 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 5SX5 · Crystal Structure of panitumumab in complex with epidermal growth factor receptor domain… · the same entry in another collection · chain N against N, TM-score 1.00
- P00533 · AlphaFold monomer V2.0 prediction for epidermal growth factor receptor (P00533) · a predicted model of the same protein · chain N 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 P00533
- Elsewhere: RCSB PDB 5SX5 · PDBe 5SX5 · UniProt P00533
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.