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Yersinia pestis plasminogen activator pla

Analyse Yersinia pestis plasminogen activator pla in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2X4M
Type: protein
Length: 1,163 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: COAGULASE/FIBRINOLYSIN
EC: 3.4.23.48
UniProt: P17811
Ligands: SO4
Pockets: 13 · best druggability 0.82

Structure

x-ray diffraction · 3 distinct chains · 1% helix, 77% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	COAGULASE/FIBRINOLYSIN (EC 3.4.23.48)	protein	293	1% helix, 75% strand	P17811
B	COAGULASE/FIBRINOLYSIN (EC 3.4.23.48)	protein	286	1% helix, 78% strand	P17811
C	COAGULASE/FIBRINOLYSIN (EC 3.4.23.48)	protein	291	0% helix, 78% strand	P17811

Ligands and binding sites

SO4 · Sulfate ion · ion · 23 copies · chains A, B, C, D
C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 14 copies · chains A, C, B, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	252	0.82	0.94	56	SO4
2	270	0.76	0.89	50	empty
3	393	0.75	0.86	45	empty
4	304	0.75	0.87	37	empty
5	814	0.69	0.75	61	C8E

Interfaces

4 interfaces between chains.

A–C · 842 Å² buried · 15 hydrogen bonds · protein-protein
B–D · 713 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 620 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 45 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

2X4M · Yersinia Pestis Plasminogen Activator Pla · the same entry in another collection · chain D against D, TM-score 1.00
P17811 · AlphaFold monomer V2.0 prediction for COAGULASE/FIBRINOLYSIN (P17811) · a predicted model of the same protein · chain C 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 P17811
Elsewhere: RCSB PDB 2X4M · PDBe 2X4M · UniProt P17811

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