MolNFT v1 · #15104 · protein

Thrombin-hirugen-L405,426

1MUE: “Thrombin-hirugen-L405,426”. X-ray diffraction, 1 ligand (CDD), 1 pocket (best druggability 0.54). MolNFT v1 #15104 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1MUE
Type: protein
Length: 287 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thrombin; Hirudin iib
EC: 3.4.21.5
UniProt: P00734, P28506
Ligands: CDD
Pockets: 1 · best druggability 0.54

Structure

x-ray diffraction · 3 distinct chains · 18% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Thrombin (EC 3.4.21.5)	protein	26	38% helix, 0% strand	P00734
B	Thrombin (EC 3.4.21.5)	protein	250	15% helix, 36% strand	P00734
C	Hirudin iib	protein	11	36% helix, 0% strand	P28506

Ligands and binding sites

CDD · 2-(6-chloro-3-{[2,2-difluoro-2-(1-oxido-2-pyridinyl)ethyl]amino}-2-oxo-1(2H)-pyrazinyl)-N-[(2-fluorophenyl)methyl]acetamide · ligand · chains B

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	240	0.54	0.77	42	CDD

Interfaces

2 interfaces between chains.

A–B · 1114 Å² buried · 25 hydrogen bonds · protein-protein
B–C · 689 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

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

Compared structures

1MUE · Thrombin-Hirugen-L405,426 · the same entry in another collection · chain B against B, TM-score 1.00
P28506 · AlphaFold monomer V2.0 prediction for hirudin-2B (P28506) · a predicted model of the same protein · chain C against A, TM-score 0.53

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 P28506
Elsewhere: RCSB PDB 1MUE · PDBe 1MUE · UniProt P00734 · UniProt P28506

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