MolNFT v1 · #39065 · protein

Crystal structure of human native protein C inhibitor

2HI9 · Plasma serine protease inhibitor: “Crystal structure of human native protein C inhibitor”. X-ray diffraction, 13 pockets (best druggability 0.70). MolNFT v1 #39065 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2HI9
Type: protein
Length: 1,056 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Plasma serine protease inhibitor
UniProt: P05154
Pockets: 13 · best druggability 0.70

Structure

x-ray diffraction · 3 distinct chains · 29% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Plasma serine protease inhibitor	protein	356	29% helix, 34% strand	P05154
B	Plasma serine protease inhibitor	protein	354	29% helix, 35% strand	P05154
C	Plasma serine protease inhibitor	protein	346	31% helix, 34% strand	P05154

Ligands and binding sites

CIT · Citric acid · additive · 3 copies · chains A, B, C
GOL · Glycerol · additive · chains B

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

Pockets

13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	399	0.70	0.82	44	empty
2	343	0.66	0.81	54	empty
3	79	0.56	0.87	22	empty
4	111	0.55	0.83	19	empty
5	248	0.54	0.76	26	empty

Interfaces

3 interfaces between chains.

B–C · 467 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 367 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 294 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

2HI9 · Crystal Structure of human native protein C inhibitor · 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 0.99

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 P05154
Elsewhere: RCSB PDB 2HI9 · PDBe 2HI9 · UniProt P05154

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