Research workbench
Structural and functional characterization of an agonistic anti-human EPHA2 monoclonal antibody
Analyse Structural and functional characterization of an agonistic anti-human EPHA2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SKJ
- Type
- protein
- Length
- 1,144 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody, light chain; Antibody, heavy chain; Ephrin type-a receptor 2
- EC
- 2.7.10.1
- UniProt
- P29317
- Pockets
- 16 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 7% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, M | Antibody, light chain | protein | 214 | 7% helix, 50% strand | — |
| H | Antibody, heavy chain | protein | 228 | 8% helix, 48% strand | — |
| I | Antibody, heavy chain | protein | 228 | 7% helix, 48% strand | — |
| E | Ephrin type-a receptor 2 (EC 2.7.10.1) | protein | 176 | 8% helix, 47% strand | P29317 |
| F | Ephrin type-a receptor 2 (EC 2.7.10.1) | protein | 84 | 10% helix, 33% strand | P29317 |
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 935 | 0.74 | 0.78 | 111 | empty |
| 2 | 851 | 0.74 | 0.78 | 102 | empty |
| 3 | 257 | 0.55 | 0.77 | 34 | empty |
| 4 | 145 | 0.53 | 0.80 | 29 | empty |
| 5 | 150 | 0.52 | 0.79 | 22 | empty |
Interfaces
10 interfaces between chains.
- M–I · 2260 Ų buried · 22 hydrogen bonds · protein-protein
- L–H · 2079 Ų buried · 22 hydrogen bonds · protein-protein
- H–E · 703 Ų buried · 7 hydrogen bonds · protein-protein
- I–F · 697 Ų buried · 8 hydrogen bonds · protein-protein
- L–M · 273 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 3SKJ · Structural And Functional Characterization of an Agonistic Anti-Human EphA2 Monoclonal… · the same entry in another collection · chain F against F, TM-score 1.00
- P29317 · AlphaFold monomer V2.0 prediction for ephrin type-a receptor 2 (P29317) · a predicted model of the same protein · chain E against A, TM-score 0.97
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 P29317
- Elsewhere: RCSB PDB 3SKJ · PDBe 3SKJ · UniProt P29317
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