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Crystal structure of the human ephrin A2 lbd and crd domains in complex with ephrin A1
Analyse Crystal structure of the human ephrin A2 lbd and crd domains in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MBW
- Type
- protein
- Length
- 413 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ephrin type-a receptor 2; Ephrin-A1
- EC
- 2.7.10.1
- UniProt
- P29317, P20827
- Ligands
- NAG, BMA, MAN, UNX
- Pockets
- 4 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ephrin type-a receptor 2 (EC 2.7.10.1) | protein | 286 | 5% helix, 41% strand | P29317 |
| B | Ephrin-A1 | protein | 127 | 9% helix, 35% strand | P20827 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar
- UNX · Unknown atom or ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 223 | 0.56 | 0.79 | 33 | empty |
| 2 | 81 | 0.47 | 0.81 | 18 | empty |
| 3 | 157 | 0.41 | 0.74 | 25 | empty |
| 4 | 51 | 0.29 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1159 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 3MBW · Crystal structure of the human ephrin A2 LBD and CRD domains in complex with ephrin A1 · the same entry in another collection · chain A against A, TM-score 1.00
- P20827 · AlphaFold monomer V2.0 prediction for ephrin-A1 (P20827) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P29317 · AlphaFold monomer V2.0 prediction for ephrin type-a receptor 2 (P29317) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P29317
- Every structure of UniProt P20827
- Elsewhere: RCSB PDB 3MBW · PDBe 3MBW · UniProt P29317 · UniProt P20827
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