MolNFT v1 · #158101 · protein
EPHA2 lbd in complex with ba-wla-yam peptide
6NK0 · Ephrin type-a receptor 2: “EPHA2 lbd in complex with ba-wla-yam peptide”. X-ray diffraction, 2 ligands (ACA, NH2), 5 pockets (best druggability 0.56). MolNFT v1 #158101 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6NK0
- Type
- protein
- Length
- 381 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ephrin type-a receptor 2; Ba-wla-yam
- EC
- 2.7.10.1
- UniProt
- P29317
- Ligands
- ACA, NH2
- Pockets
- 5 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ephrin type-a receptor 2 (EC 2.7.10.1) | protein | 178 | 10% helix, 46% strand | P29317 |
| B | Ephrin type-a receptor 2 (EC 2.7.10.1) | protein | 181 | 8% helix, 45% strand | P29317 |
| C, D | Ba-wla-yam | protein | 11 | 0% helix, 18% strand | — |
Ligands and binding sites
- ACA · 6-aminohexanoic acid · ligand · chains A
- NH2 · Amino group · ion · 2 copies · chains C, B, D
- GOL · Glycerol · additive · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 168 | 0.56 | 0.81 | 26 | empty |
| 2 | 102 | 0.54 | 0.83 | 17 | empty |
| 3 | 100 | 0.40 | 0.77 | 18 | empty |
| 4 | 88 | 0.37 | 0.76 | 15 | GOL |
| 5 | 52 | 0.29 | 0.76 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–B · 962 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 844 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 837 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 modified (disulfide, nonstandard).
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 P29317
- Elsewhere: RCSB PDB 6NK0 · PDBe 6NK0 · UniProt P29317
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