Research workbench
Anti-EPHA1 JD1-1 vh domain
Analyse Anti-EPHA1 JD1-1 vh domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OMN
- Type
- protein
- Length
- 372 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- JD1-1 vh domain
- Pockets
- 5 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | JD1-1 vh domain | protein | 124 | 10% helix, 50% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 229 | 0.57 | 0.79 | 34 | GOL, IMD |
| 2 | 114 | 0.40 | 0.75 | 25 | IMD |
| 3 | 74 | 0.40 | 0.79 | 18 | empty |
| 4 | 65 | 0.36 | 0.78 | 20 | IMD |
| 5 | 53 | 0.26 | 0.73 | 15 | IMD |
Interfaces
3 interfaces between chains.
- B–C · 817 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 580 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 528 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7OMN · Anti-EphA1 JD1-1 VH domain · 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
- Elsewhere: RCSB PDB 7OMN · PDBe 7OMN
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