Research workbench
Crystal structure of the human EPHA4 ectodomain in complex with human EPHRINB3
Analyse Crystal structure of the human EPHA4 ectodomain in complex with human EPHRINB3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BKF
- Type
- protein
- Length
- 1,292 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ephrin type-a receptor 4; Ephrin-B3
- EC
- 2.7.10.1
- UniProt
- P54764, Q15768
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ephrin type-a receptor 4 (EC 2.7.10.1) | protein | 505 | 2% helix, 39% strand | P54764 |
| C, D | Ephrin-B3 | protein | 141 | 6% helix, 28% strand | Q15768 |
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 602 | 0.74 | 0.81 | 77 | empty |
| 2 | 534 | 0.71 | 0.80 | 63 | empty |
| 3 | 66 | 0.62 | 0.92 | 25 | empty |
| 4 | 152 | 0.50 | 0.79 | 25 | empty |
| 5 | 103 | 0.49 | 0.81 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–D · 1253 Ų buried · 45 hydrogen bonds · protein-protein
- B–C · 1201 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 974 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 1 isopeptide (disulfide, isopeptide).
Compared structures
- 4BKF · crystal structure of the human EphA4 ectodomain in complex with human ephrinB3 · the same entry in another collection · chain D against D, TM-score 1.00
- Q15768 · AlphaFold monomer V2.0 prediction for ephrin-B3 (Q15768) · a predicted model of the same protein · chain C against A, TM-score 0.95
- P54764 · AlphaFold monomer V2.0 prediction for ephrin type-a receptor 4 (P54764) · a predicted model of the same protein · chain B against A, TM-score 0.73
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 P54764
- Every structure of UniProt Q15768
- Elsewhere: RCSB PDB 4BKF · PDBe 4BKF · UniProt P54764 · UniProt Q15768
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