Research workbench
Crystal structure of NK2 in complex with fractionated heparin DP10
Analyse Crystal structure of NK2 in complex with fractionated heparin DP10 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SP8
- Type
- protein
- Length
- 511 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hepatocyte growth factor alpha chain
- UniProt
- P14210
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hepatocyte growth factor alpha chain | protein | 255 | 8% helix, 24% strand | P14210 |
| B | Hepatocyte growth factor alpha chain | protein | 256 | 10% helix, 25% strand | P14210 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 10 copies · chains A, B
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 4 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 4 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
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 | 874 | 0.71 | 0.76 | 96 | MRD |
| 2 | 139 | 0.43 | 0.76 | 26 | empty |
| 3 | 99 | 0.35 | 0.74 | 20 | empty |
| 4 | 69 | 0.35 | 0.78 | 13 | empty |
| 5 | 52 | 0.30 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 354 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 3SP8 · Crystal structure of NK2 in complex with fractionated Heparin DP10 · the same entry in another collection · chain A against A, TM-score 1.00
- P14210 · AlphaFold monomer V2.0 prediction for hepatocyte growth factor (P14210) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P14210
- Elsewhere: RCSB PDB 3SP8 · PDBe 3SP8 · UniProt P14210
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