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Crystal structure of EPHB1
Analyse Crystal structure of EPHB1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZFX
- Type
- protein
- Length
- 2,332 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ephrin type-B receptor 1
- EC
- 2.7.10.1
- UniProt
- P54762
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.66
Structure
x-ray diffraction · 9 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ephrin type-B receptor 1 (EC 2.7.10.1) | protein | 267 | 40% helix, 17% strand | P54762 |
| B | Ephrin type-B receptor 1 (EC 2.7.10.1) | protein | 254 | 44% helix, 18% strand | P54762 |
| C | Ephrin type-B receptor 1 (EC 2.7.10.1) | protein | 248 | 45% helix, 14% strand | P54762 |
| D | Ephrin type-B receptor 1 (EC 2.7.10.1) | protein | 265 | 41% helix, 17% strand | P54762 |
| E | Ephrin type-B receptor 1 (EC 2.7.10.1) | protein | 262 | 41% helix, 18% strand | P54762 |
| F | Ephrin type-B receptor 1 (EC 2.7.10.1) | protein | 254 | 43% helix, 19% strand | P54762 |
| G | Ephrin type-B receptor 1 (EC 2.7.10.1) | protein | 253 | 43% helix, 18% strand | P54762 |
| H | Ephrin type-B receptor 1 (EC 2.7.10.1) | protein | 266 | 40% helix, 17% strand | P54762 |
| I | Ephrin type-B receptor 1 (EC 2.7.10.1) | protein | 263 | 41% helix, 18% strand | P54762 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 623 | 0.66 | 0.76 | 55 | empty |
| 2 | 389 | 0.65 | 0.79 | 40 | empty |
| 3 | 510 | 0.64 | 0.76 | 45 | empty |
| 4 | 445 | 0.64 | 0.77 | 51 | empty |
| 5 | 501 | 0.62 | 0.75 | 58 | empty |
Interfaces
12 interfaces between chains.
- A–I · 392 Ų buried · 2 hydrogen bonds · protein-protein
- E–I · 374 Ų buried · 6 hydrogen bonds · protein-protein
- B–F · 341 Ų buried · 4 hydrogen bonds · protein-protein
- G–I · 338 Ų buried · 3 hydrogen bonds · protein-protein
- C–H · 295 Ų buried · 0 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 P54762
- Elsewhere: RCSB PDB 3ZFX · PDBe 3ZFX · UniProt P54762
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