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Structure of plasmin and peptide complex

Analyse Structure of plasmin and peptide complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6Q1U
Type: protein
Length: 516 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Plasminogen; Gly-arg-ala-tyr-lys-ser-lys-pro-pro-ile-ala-phe-pro-asp
EC: 3.4.21.7
UniProt: P00747
Ligands: WMH
Pockets: 4 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 10% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Plasminogen (EC 3.4.21.7)	protein	244	10% helix, 37% strand	P00747
C, D	Gly-arg-ala-tyr-lys-ser-lys-pro-pro-ile-ala-phe-pro-asp	protein	14	0% helix, 29% strand	—

Ligands and binding sites

WMH · 1-methyl-1H-1,2,3-triazole · ligand · 2 copies · chains C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	328	0.82	0.92	39	empty
2	200	0.50	0.76	36	empty
3	62	0.32	0.75	14	empty
4	61	0.29	0.74	14	empty

Interfaces

5 interfaces between chains.

A–C · 632 Å² buried · 15 hydrogen bonds · protein-protein
B–D · 628 Å² buried · 16 hydrogen bonds · protein-protein
B–C · 336 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 333 Å² buried · 0 hydrogen bonds · protein-protein
A–B · 275 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide, 4 covalent (disulfide, covalent ligand).

Compared structures

6Q1U · Structure of plasmin and peptide complex · the same entry in another collection · chain A against A, TM-score 1.00
P00747 · AlphaFold monomer V2.0 prediction for plasminogen (P00747) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 6Q1U · PDBe 6Q1U · UniProt P00747

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