MolNFT v1 · #158126 · protein
EPHA2 lbd in complex with ba-wla-yskbio peptide
6NKP · Ephrin type-a receptor 2: “EPHA2 lbd in complex with ba-wla-yskbio peptide”. X-ray diffraction, 1 ligand (BTN), 4 pockets (best druggability 0.62). MolNFT v1 #158126 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6NKP
- Type
- protein
- Length
- 377 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ephrin type-a receptor 2; Ba-wla-yskbio peptide
- EC
- 2.7.10.1
- UniProt
- P29317
- Ligands
- BTN
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ephrin type-a receptor 2 (EC 2.7.10.1) | protein | 175 | 8% helix, 46% strand | P29317 |
| B | Ephrin type-a receptor 2 (EC 2.7.10.1) | protein | 179 | 8% helix, 44% strand | P29317 |
| C | Ba-wla-yskbio peptide | protein | 11 | 0% helix, 18% strand | — |
| D | Ba-wla-yskbio peptide | protein | 12 | 0% helix, 17% strand | — |
Ligands and binding sites
- BTN · Biotin · ligand · chains A, B
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 | 501 | 0.62 | 0.75 | 39 | BTN |
| 2 | 108 | 0.45 | 0.78 | 24 | empty |
| 3 | 95 | 0.43 | 0.78 | 24 | empty |
| 4 | 58 | 0.33 | 0.77 | 14 | empty |
Interfaces
3 interfaces between chains.
- B–D · 849 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 836 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 764 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 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 6NKP · PDBe 6NKP · UniProt P29317
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