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Structural basis for the conformational modulation

Analyse Structural basis for the conformational modulation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4A5T
Type: protein
Length: 767 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Plasminogen
EC: 3.4.21.7
UniProt: P00747
Ligands: NGA, GAL, SIA, CL
Pockets: 7 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 7% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
S	Plasminogen (EC 3.4.21.7)	protein	767	7% helix, 25% strand	P00747

Ligands and binding sites

NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · chains S
GAL · beta-D-galactopyranose · sugar
SIA · N-acetyl-alpha-neuraminic acid · sugar
CL · Chloride ion · ion · 2 copies · chains S

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

Pockets

7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1042	0.75	0.78	86	empty
2	789	0.66	0.74	93	CL
3	349	0.66	0.80	40	empty
4	114	0.53	0.82	24	empty
5	87	0.41	0.78	21	empty

Modifications

Observed in the structure: 24 disulfide, 1 glycan (disulfide, O-glycosylation).

Compared structures

4A5T · Structural basis for the conformational modulation · the same entry in another collection · chain S against S, TM-score 1.00
P00747 · AlphaFold monomer V2.0 prediction for plasminogen (P00747) · a predicted model of the same protein · chain S against A, TM-score 0.72

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 P00747
Elsewhere: RCSB PDB 4A5T · PDBe 4A5T · UniProt P00747

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