Research workbench
Crystal structure of the EPHA2 intracellular kd-SAM domains
Analyse Crystal structure of the EPHA2 intracellular kd-SAM domains in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KJA
- Type
- protein
- Length
- 713 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ephrin type-a receptor 2
- EC
- 2.7.10.1
- UniProt
- P29317
- Ligands
- ACP, MG
- Pockets
- 9 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ephrin type-a receptor 2 (EC 2.7.10.1) | protein | 364 | 45% helix, 13% strand | P29317 |
| B | Ephrin type-a receptor 2 (EC 2.7.10.1) | protein | 349 | 46% helix, 13% strand | P29317 |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 593 | 0.68 | 0.77 | 53 | GOL, ACP |
| 2 | 272 | 0.62 | 0.80 | 30 | ACP, MG |
| 3 | 224 | 0.55 | 0.78 | 36 | GOL |
| 4 | 99 | 0.43 | 0.78 | 22 | empty |
| 5 | 102 | 0.39 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 682 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
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 7KJA · PDBe 7KJA · UniProt P29317
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