MolNFT v1 · #142062 · protein
Crystal structure of EPHA6/ODIN complex
5ZRY · Ankyrin repeat and SAM domain-containing protein 1A,EPHRIN…: “Crystal structure of EPHA6/ODIN complex”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.76). MolNFT v1 #142062 on GenesisL1: 3D structure, binding…
- PDB
- 5ZRY
- Type
- protein
- Length
- 330 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ankyrin repeat and SAM domain-containing protein 1A,EPHRIN type-a receptor 6
- EC
- 2.7.10.1
- UniProt
- P59672, Q62413
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ankyrin repeat and SAM domain-containing protein 1A,EPHRIN type-a receptor 6 (EC 2.7.10.1) | protein | 169 | 51% helix, 4% strand | P59672, Q62413 |
| B | Ankyrin repeat and SAM domain-containing protein 1A,EPHRIN type-a receptor 6 (EC 2.7.10.1) | protein | 161 | 52% helix, 2% strand | P59672, Q62413 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1007 | 0.76 | 0.78 | 68 | SO4, EPE |
| 2 | 203 | 0.56 | 0.79 | 35 | empty |
| 3 | 78 | 0.48 | 0.82 | 15 | empty |
| 4 | 163 | 0.43 | 0.74 | 28 | empty |
| 5 | 56 | 0.34 | 0.77 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 644 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 5ZRY · Crystal Structure of EphA6/Odin Complex · the same entry in another collection · chain A against A, TM-score 1.00
- P59672 · AlphaFold monomer V2.0 prediction for ankyrin repeat and SAM domain- containing protein… · a predicted model of the same protein · chain B against A, TM-score 0.76
- Q62413 · AlphaFold monomer V2.0 prediction for ephrin type-a receptor 6 (Q62413) · a predicted model of the same protein · chain B against A, TM-score 0.55
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 P59672
- Every structure of UniProt Q62413
- Elsewhere: RCSB PDB 5ZRY · PDBe 5ZRY · UniProt P59672 · UniProt Q62413
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