MolNFT v1 · #28808 · protein

Thrombin inhibitor complex

1YPJ · Thrombin light chain: “Thrombin inhibitor complex”. X-ray diffraction, 1 ligand (UIB), 2 pockets (best druggability 0.55). MolNFT v1 #28808 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1YPJ
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
EC: 3.4.21.5
UniProt: P00734, P28504
Ligands: UIB
Pockets: 2 · best druggability 0.55

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Thrombin light chain (EC 3.4.21.5)	protein	27	37% helix, 0% strand	P00734
H	Thrombin heavy chain (EC 3.4.21.5)	protein	251	15% helix, 35% strand	P00734
I	Hirudin	protein	10	30% helix, 0% strand	P28504

Ligands and binding sites

UIB · (1r,3as,4r,8as,8br)-4-{5-(phenyl[1,3]dioxol-5-ylmethyl)-4-ethyl-2,3,3-trimethyl-6-oxo-octahydro-pyrrolo[3,4-c]pyrrol-1-yl}-benzamidine · ligand · chains H

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	273	0.55	0.76	41	UIB
2	51	0.31	0.77	15	empty

Interfaces

2 interfaces between chains.

L–H · 1101 Å² buried · 27 hydrogen bonds · protein-protein
H–I · 609 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

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

Compared structures

1YPJ · Thrombin Inhibitor Complex · the same entry in another collection · chain L against L, TM-score 1.00
P28504 · AlphaFold monomer V2.0 prediction for hirudin-2 (P28504) · a predicted model of the same protein · chain I against A, TM-score 0.55

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 P28504
Elsewhere: RCSB PDB 1YPJ · PDBe 1YPJ · UniProt P00734 · UniProt P28504

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