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Crystal structure of the heparin cofactor II-S195A thrombin complex

Analyse Crystal structure of the heparin cofactor II-S195A thrombin complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1JMO
Type: protein
Length: 733 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thrombin, light chain; Thrombin, heavy chain; Heparin cofactor II
EC: 3.4.21.5
UniProt: P00734, P05546
Ligands: NAG, NA
Pockets: 9 · best druggability 0.81

Structure

x-ray diffraction · 3 distinct chains · 26% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Thrombin, light chain	protein	47	30% helix, 0% strand	P00734
H	Thrombin, heavy chain (EC 3.4.21.5)	protein	259	15% helix, 35% strand	P00734
A	Heparin cofactor II	protein	427	32% helix, 28% strand	P05546

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains H, A
NA · Sodium ion · metal · chains H
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 5 copies · chains H, A

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

Pockets

9 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	887	0.81	0.83	74	empty
2	380	0.61	0.77	42	empty
3	184	0.56	0.80	32	empty
4	136	0.53	0.81	21	empty
5	107	0.47	0.80	20	empty

Interfaces

2 interfaces between chains.

H–A · 1861 Å² buried · 38 hydrogen bonds · protein-protein
L–H · 1804 Å² buried · 39 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 3 glycan, 2 modified (disulfide, N-glycosylation, sulfation).

Compared structures

1JMO · Crystal Structure of the Heparin Cofactor II-S195A Thrombin Complex · the same entry in another collection · chain L against L, TM-score 1.00
P05546 · AlphaFold monomer V2.0 prediction for heparin cofactor 2 (P05546) · a predicted model of the same protein · chain A against A, TM-score 0.89

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 P00734
Every structure of UniProt P05546
Elsewhere: RCSB PDB 1JMO · PDBe 1JMO · UniProt P00734 · UniProt P05546

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