MolNFT v1 · #61858 · protein

Crystal structure of cleaved pci bound to heparin

3DY0 · N-terminus plasma serine protease inhibitor: “Crystal structure of cleaved pci bound to heparin”. X-ray diffraction, 3 ligands (IDS, SGN, NO3), 3 pockets (best druggability 0.53). MolNFT v1 #61858 on GenesisL1: 3D structure, binding…

PDB: 3DY0
Type: protein
Length: 355 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: N-terminus plasma serine protease inhibitor; C-terminus plasma serine protease inhibitor
UniProt: P05154
Ligands: IDS, SGN, NO3
Pockets: 3 · best druggability 0.53

Structure

x-ray diffraction · 2 distinct chains · 30% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	N-terminus plasma serine protease inhibitor	protein	327	33% helix, 36% strand	P05154
B	C-terminus plasma serine protease inhibitor	protein	28	0% helix, 61% strand	P05154

Ligands and binding sites

IDS · 2-O-sulfo-alpha-L-idopyranuronic acid · sugar · 3 copies · chains A
SGN · 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · sugar · 2 copies · chains A
NO3 · Nitrate ion · ion · 2 copies · chains A, B
GOL · Glycerol · additive · chains A, B

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

Pockets

3 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	283	0.53	0.75	26	GOL
2	63	0.32	0.76	17	empty
3	53	0.28	0.75	17	empty

Interfaces

1 interface between chains.

A–B · 2261 Å² buried · 29 hydrogen bonds · protein-protein

Compared structures

3DY0 · Crystal Structure of Cleaved PCI Bound to Heparin · the same entry in another collection · chain A against A, TM-score 1.00
P05154 · AlphaFold monomer V2.0 prediction for plasma serine protease inhibitor (P05154) · a predicted model of the same protein · chain A against A, TM-score 0.90

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 P05154
Elsewhere: RCSB PDB 3DY0 · PDBe 3DY0 · UniProt P05154

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