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Crystal structure of cleaved protein C inhibitor

Analyse Crystal structure of cleaved protein C inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1LQ8
Type: protein
Length: 1,431 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Plasma serine protease inhibitor
UniProt: P05154
Ligands: NAG, MAN, NDG
Pockets: 14 · best druggability 0.71

Structure

x-ray diffraction · 5 distinct chains · 29% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Plasma serine protease inhibitor	protein	329	32% helix, 36% strand	P05154
B, D, H	Plasma serine protease inhibitor	protein	29	0% helix, 59% strand	P05154
C	Plasma serine protease inhibitor	protein	328	30% helix, 36% strand	P05154
F	Plasma serine protease inhibitor	protein	28	0% helix, 61% strand	P05154
G	Plasma serine protease inhibitor	protein	330	32% helix, 35% strand	P05154

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B, C, D, E, G, H
MAN · alpha-D-mannopyranose · sugar · 3 copies · chains G
NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 2 copies · chains A, H
IPA · Isopropyl alcohol · additive · 3 copies · chains A, C, G

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

Pockets

14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	860	0.71	0.76	74	NAG
2	683	0.70	0.77	50	empty
3	369	0.70	0.82	36	empty
4	577	0.67	0.77	36	empty
5	501	0.66	0.78	44	NAG

Interfaces

10 interfaces between chains.

E–F · 2256 Å² buried · 35 hydrogen bonds · protein-protein
C–D · 2219 Å² buried · 27 hydrogen bonds · protein-protein
A–B · 2216 Å² buried · 28 hydrogen bonds · protein-protein
G–H · 2200 Å² buried · 28 hydrogen bonds · protein-protein
A–C · 434 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 glycan (N-glycosylation).

Compared structures

1LQ8 · Crystal structure of cleaved protein C inhibitor · the same entry in another collection · chain H against H, TM-score 1.00
P05154 · AlphaFold monomer V2.0 prediction for plasma serine protease inhibitor (P05154) · a predicted model of the same protein · chain B 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 1LQ8 · PDBe 1LQ8 · UniProt P05154

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