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Crystal structure of a signaling molecule

Analyse Crystal structure of a signaling molecule in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2QMS
Type: protein
Length: 452 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Growth factor receptor-bound protein 7
UniProt: Q14451
Ligands: SO4
Pockets: 7 · best druggability 0.50

Structure

x-ray diffraction · 1 distinct chain · 19% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Growth factor receptor-bound protein 7	protein	113	19% helix, 32% strand	Q14451

Ligands and binding sites

SO4 · Sulfate ion · ion · 7 copies · chains A, B, C, D

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

Pockets

7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	212	0.50	0.76	27	empty
2	171	0.43	0.74	25	empty
3	85	0.32	0.73	14	empty
4	56	0.32	0.76	10	empty
5	50	0.31	0.77	15	empty

Interfaces

3 interfaces between chains.

C–D · 578 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 483 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 478 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

2QMS · Crystal structure of a signaling molecule · the same entry in another collection · chain A against A, TM-score 1.00
Q14451 · AlphaFold monomer V2.0 prediction for growth factor receptor-bound protein 7 (Q14451) · a predicted model of the same protein · chain A against A, TM-score 0.90

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 Q14451
Elsewhere: RCSB PDB 2QMS · PDBe 2QMS · UniProt Q14451

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