MolNFT v1 · #134202 · protein
Crystal structure of panitumumab in complex with epidermal growth factor receptor domain 3.
5SX4 · Panitumumab Fab light chain: “Crystal structure of panitumumab in complex with epidermal growth factor receptor domain 3.”. X-ray diffraction, 1 ligand (SO4), 19 pockets (best druggability 0.57). MolNFT v1 #134202 on GenesisL1: 3D…
- 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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