MolNFT v1 · #115743 · protein

The structure of the NK1 fragment of HGF/SF complexed with mops

5CSQ · Hepatocyte growth factor: “The structure of the NK1 fragment of HGF/SF complexed with mops”. X-ray diffraction, 4 pockets (best druggability 0.69). MolNFT v1 #115743 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5CSQ
Type: protein
Length: 346 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hepatocyte growth factor
UniProt: P14210
Pockets: 4 · best druggability 0.69

Structure

x-ray diffraction · 2 distinct chains · 10% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hepatocyte growth factor	protein	173	9% helix, 31% strand	P14210
B	Hepatocyte growth factor	protein	173	12% helix, 30% strand	P14210

Ligands and binding sites

MPO · 3[N-morpholino]propane sulfonic acid · additive · 2 copies · 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	471	0.69	0.80	58	empty
2	292	0.55	0.76	49	empty
3	94	0.46	0.80	35	empty
4	124	0.40	0.75	24	empty

Interfaces

1 interface between chains.

A–B · 1271 Å² buried · 23 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

5CSQ · The structure of the NK1 fragment of HGF/SF complexed with MOPS · 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 0.59

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 5CSQ · PDBe 5CSQ · UniProt P14210

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