MolNFT v1 · #94957 · protein

Crystal structure of pai-1 in complex with gallate

4IC0 · Plasminogen activator inhibitor 1: “Crystal structure of pai-1 in complex with gallate”. X-ray diffraction, 1 ligand (GDE), 16 pockets (best druggability 0.64). MolNFT v1 #94957 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 4IC0
Type: protein
Length: 1,449 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Plasminogen activator inhibitor 1
UniProt: P05121
Ligands: GDE
Pockets: 16 · best druggability 0.64

Structure

x-ray diffraction · 3 distinct chains · 31% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Plasminogen activator inhibitor 1	protein	366	31% helix, 32% strand	P05121
B	Plasminogen activator inhibitor 1	protein	358	31% helix, 32% strand	P05121
D	Plasminogen activator inhibitor 1	protein	359	31% helix, 32% strand	P05121

Ligands and binding sites

GDE · 3,4,5-trihydroxybenzoic acid · ligand · 2 copies · chains A, C

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

Pockets

16 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	170	0.64	0.85	29	empty
2	161	0.64	0.85	28	empty
3	153	0.63	0.85	29	GDE
4	140	0.62	0.85	28	GDE
5	70	0.44	0.82	15	empty

Interfaces

3 interfaces between chains.

C–D · 214 Å² buried · 1 hydrogen bond · protein-protein
A–B · 195 Å² buried · 0 hydrogen bonds · protein-protein
B–D · 40 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 3 covalent (covalent ligand).

Compared structures

4IC0 · Crystal Structure of PAI-1 in Complex with Gallate · 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 D 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 4IC0 · PDBe 4IC0 · UniProt P05121

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