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Crystal structure of upa in complex with S2444

Analyse Crystal structure of upa in complex with S2444 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5WXS
Type: protein
Length: 246 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Urokinase-type plasminogen activator chain B
EC: 3.4.21.73
UniProt: P00749
Ligands: 7YF
Pockets: 1 · best druggability 0.44

Structure

x-ray diffraction · 1 distinct chain · 11% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
U	Urokinase-type plasminogen activator chain B (EC 3.4.21.73)	protein	246	11% helix, 38% strand	P00749

Ligands and binding sites

7YF · (2R)-N-[2-[[(2S)-5-carbamimidamido-1-oxidanylidene-pentan-2-yl]amino]-2-oxidanylidene-ethyl]-5-oxidanylidene-1,2-dihydropyrrole-2-carboxamide · ligand · chains U

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	128	0.44	0.77	34	7YF

Modifications

Observed in the structure: 5 disulfide, 1 covalent (disulfide, covalent ligand).

Compared structures

5WXS · Crystal structure of uPA in complex with S2444 · the same entry in another collection · chain U against U, TM-score 1.00

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 P00749
Elsewhere: RCSB PDB 5WXS · PDBe 5WXS · UniProt P00749

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