MolNFT v1 · #179900 · protein
Crystal structure of the EPHA2 S901E mutant intracellular kd-SAM domains
7KJC · Ephrin type-a receptor 2: “Crystal structure of the EPHA2 S901E mutant intracellular kd-SAM domains”. X-ray diffraction, 2 ligands (ACP, MG), 7 pockets (best druggability 0.72). MolNFT v1 #179900 on GenesisL1: 3D structure, binding…
- PDB
- 7KJC
- Type
- protein
- Length
- 726 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
- 7 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ephrin type-a receptor 2 (EC 2.7.10.1) | protein | 376 | 43% helix, 14% strand | P29317 |
| B | Ephrin type-a receptor 2 (EC 2.7.10.1) | protein | 350 | 45% 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 · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 469 | 0.72 | 0.82 | 49 | ACP, MG |
| 2 | 463 | 0.66 | 0.78 | 46 | ACP |
| 3 | 326 | 0.62 | 0.79 | 53 | GOL |
| 4 | 148 | 0.42 | 0.75 | 18 | empty |
| 5 | 93 | 0.41 | 0.77 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 704 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 7KJC · Crystal structure of the EphA2 S901E mutant intracellular KD-SAM domains · the same entry in another collection · chain A against A, 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 B against A, TM-score 0.79
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 7KJC · PDBe 7KJC · UniProt P29317
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