Research workbench
Crystal structure of panitumumab in complex with epidermal growth factor receptor domain 3.
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
- 5SX4
- Type
- protein
- Length
- 1,218 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
- 19 · best druggability 0.57
Structure
x-ray diffraction · 5 distinct chains · 10% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I, L | Panitumumab Fab light chain | protein | 213 | 6% helix, 52% strand | — |
| J | Panitumumab Fab heavy chain | protein | 205 | 6% helix, 56% strand | — |
| H | Panitumumab Fab heavy chain | protein | 210 | 6% helix, 54% strand | — |
| M | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 191 | 15% helix, 21% strand | P00533 |
| N | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 186 | 18% helix, 19% strand | P00533 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains I, M, L, N, H
- 1PE · Pentaethylene glycol · additive · 2 copies · chains I, J, L, H
- GOL · Glycerol · additive · chains I
- EDO · 1,2-ethanediol · additive · chains H, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.57 | 0.84 | 31 | empty |
| 2 | 442 | 0.57 | 0.74 | 61 | 1PE |
| 3 | 357 | 0.53 | 0.73 | 54 | 1PE |
| 4 | 100 | 0.43 | 0.78 | 21 | EDO |
| 5 | 77 | 0.42 | 0.80 | 18 | empty |
Interfaces
7 interfaces between chains.
- L–H · 1693 Ų buried · 10 hydrogen bonds · protein-protein
- I–J · 1676 Ų buried · 11 hydrogen bonds · protein-protein
- J–M · 608 Ų buried · 11 hydrogen bonds · protein-protein
- H–N · 593 Ų buried · 12 hydrogen bonds · protein-protein
- L–N · 365 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide (disulfide).
Compared structures
- 5SX4 · 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 0.98
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 5SX4 · PDBe 5SX4 · UniProt P00533
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