Research workbench
Ligand binding domain of EPHA7
Analyse Ligand binding domain of EPHA7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NRU
- Type
- protein
- Length
- 1,902 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ephrin receptor
- EC
- 2.7.10.1
- UniProt
- B7ZLK0
- Ligands
- SO4, CL
- Pockets
- 20 · best druggability 0.66
Structure
x-ray diffraction · 12 distinct chains · 4% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ephrin receptor (EC 2.7.10.1) | protein | 159 | 2% helix, 50% strand | B7ZLK0 |
| B | Ephrin receptor (EC 2.7.10.1) | protein | 158 | 2% helix, 49% strand | B7ZLK0 |
| C | Ephrin receptor (EC 2.7.10.1) | protein | 160 | 4% helix, 49% strand | B7ZLK0 |
| D | Ephrin receptor (EC 2.7.10.1) | protein | 160 | 4% helix, 49% strand | B7ZLK0 |
| E | Ephrin receptor (EC 2.7.10.1) | protein | 163 | 4% helix, 50% strand | B7ZLK0 |
| F | Ephrin receptor (EC 2.7.10.1) | protein | 156 | 2% helix, 52% strand | B7ZLK0 |
| G | Ephrin receptor (EC 2.7.10.1) | protein | 160 | 6% helix, 51% strand | B7ZLK0 |
| H | Ephrin receptor (EC 2.7.10.1) | protein | 157 | 4% helix, 50% strand | B7ZLK0 |
| I | Ephrin receptor (EC 2.7.10.1) | protein | 160 | 4% helix, 51% strand | B7ZLK0 |
| J | Ephrin receptor (EC 2.7.10.1) | protein | 161 | 6% helix, 50% strand | B7ZLK0 |
| K | Ephrin receptor (EC 2.7.10.1) | protein | 155 | 4% helix, 52% strand | B7ZLK0 |
| L | Ephrin receptor (EC 2.7.10.1) | protein | 153 | 4% helix, 49% strand | B7ZLK0 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 10 copies · chains A, C, G, B, D, E, J, K, L
- CL · Chloride ion · ion · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 510 | 0.66 | 0.78 | 68 | SO4 |
| 2 | 405 | 0.66 | 0.79 | 62 | SO4 |
| 3 | 421 | 0.65 | 0.78 | 61 | empty |
| 4 | 398 | 0.62 | 0.77 | 49 | empty |
| 5 | 351 | 0.58 | 0.76 | 41 | empty |
Interfaces
17 interfaces between chains.
- E–I · 904 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 893 Ų buried · 16 hydrogen bonds · protein-protein
- K–L · 889 Ų buried · 21 hydrogen bonds · protein-protein
- J–K · 773 Ų buried · 7 hydrogen bonds · protein-protein
- C–J · 753 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 23 disulfide (disulfide).
Compared structures
- 3NRU · Ligand binding domain of EPHA7 · the same entry in another collection · chain A against A, TM-score 1.00
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 B7ZLK0
- Elsewhere: RCSB PDB 3NRU · PDBe 3NRU · UniProt B7ZLK0
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