MolNFT v1 · #71356 · protein
Crystal structure of the human ephrin A2 lbd and crd domains in complex with ephrin A1
3MBW · Ephrin type-a receptor 2: “Crystal structure of the human ephrin A2 lbd and crd domains in complex with ephrin A1”. X-ray diffraction, 4 ligands (NAG, BMA, MAN), 4 pockets (best druggability 0.56). MolNFT v1 #71356 on GenesisL1: 3D…
- 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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