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Hhp-C in complex with glycosaminoglycan mimic sos

Analyse Hhp-C in complex with glycosaminoglycan mimic sos in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7PGN
Type: protein
Length: 875 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hedgehog-interacting protein
UniProt: Q96QV1
Ligands: GU4, YYJ, CA
Pockets: 12 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 5% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hedgehog-interacting protein	protein	437	4% helix, 40% strand	Q96QV1
B	Hedgehog-interacting protein	protein	438	5% helix, 39% strand	Q96QV1

Ligands and binding sites

GU4 · 2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose · ligand · 4 copies · chains A, B
YYJ · 1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose · ligand · 4 copies · chains A, B
CA · Calcium ion · metal · 2 copies · chains A, B
GOL · Glycerol · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	813	0.81	0.84	69	CA
2	843	0.79	0.82	72	CA
3	209	0.73	0.89	37	empty
4	248	0.68	0.84	42	empty
5	231	0.54	0.78	31	empty

Interfaces

1 interface between chains.

A–B · 1053 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 22 disulfide, 1 covalent (disulfide, covalent ligand).

Compared structures

7PGN · HHP-C in complex with glycosaminoglycan mimic SOS · the same entry in another collection · chain A against A, TM-score 1.00
Q96QV1 · AlphaFold monomer V2.0 prediction for hedgehog-interacting protein (Q96QV1) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q96QV1
Elsewhere: RCSB PDB 7PGN · PDBe 7PGN · UniProt Q96QV1

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