Research workbench

Human thrombin hirugen inhibitor complex

Analyse Human thrombin hirugen inhibitor complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2JH5
Type: protein
Length: 288 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thrombin light chain; Thrombin heavy chain; Hirudin iiia
EC: 3.4.21.5
UniProt: P00734, P28507
Ligands: 895, CA, NA
Pockets: 2 · best druggability 0.57

Structure

x-ray diffraction · 3 distinct chains · 17% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	Thrombin light chain (EC 3.4.21.5)	protein	28	36% helix, 0% strand	P00734
D	Thrombin heavy chain (EC 3.4.21.5)	protein	250	14% helix, 36% strand	P00734
H	Hirudin iiia	protein	10	30% helix, 0% strand	P28507

Ligands and binding sites

895 · 2-(5-chloro-2-thienyl)-N-{(3S)-1-[(1S)-1-methyl-2-morpholin-4-yl-2-oxoethyl]-2-oxopyrrolidin-3-yl}ethenesulfonamide · ligand · chains D
CA · Calcium ion · metal · chains D
NA · Sodium ion · metal · chains D

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

Pockets

2 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	274	0.57	0.77	39	895
2	51	0.29	0.76	11	empty

Interfaces

2 interfaces between chains.

C–D · 1145 Å² buried · 26 hydrogen bonds · protein-protein
D–H · 642 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 1 modified (disulfide, sulfation).

Compared structures

2JH5 · Human Thrombin Hirugen Inhibitor complex · the same entry in another collection · chain C against C, TM-score 1.00
P28507 · AlphaFold monomer V2.0 prediction for hirudin-3A (P28507) · a predicted model of the same protein · chain H against A, TM-score 0.56

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 P28507
Elsewhere: RCSB PDB 2JH5 · PDBe 2JH5 · UniProt P00734 · UniProt P28507

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