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A novel pai-I inhibitor and its structural mechanism

Analyse A novel pai-I inhibitor and its structural mechanism in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3UT3
Type: protein
Length: 1,455 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Plasminogen activator inhibitor 1
UniProt: P05121
Ligands: EMJ
Pockets: 19 · best druggability 0.74

Structure

x-ray diffraction · 3 distinct chains · 30% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Plasminogen activator inhibitor 1	protein	367	31% helix, 32% strand	P05121
B, D	Plasminogen activator inhibitor 1	protein	360	30% helix, 32% strand	P05121
C	Plasminogen activator inhibitor 1	protein	368	30% helix, 31% strand	P05121

Ligands and binding sites

EMJ · 2,5-dihydroxy-3-undecylcyclohexa-2,5-diene-1,4-dione · ligand · chains B

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

Pockets

19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	898	0.74	0.78	85	empty
2	638	0.70	0.78	60	empty
3	471	0.67	0.79	59	empty
4	156	0.62	0.84	30	EMJ
5	148	0.61	0.84	25	empty

Interfaces

3 interfaces between chains.

A–C · 908 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 854 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 819 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

3UT3 · A novel PAI-I inhibitor and its structural mechanism · the same entry in another collection · chain A against A, TM-score 1.00
P05121 · AlphaFold monomer V2.0 prediction for plasminogen activator inhibitor 1 (P05121) · a predicted model of the same protein · chain B 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 P05121
Elsewhere: RCSB PDB 3UT3 · PDBe 3UT3 · UniProt P05121

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