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Thrombin in complex with inhibitor

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

PDB: 4BAQ
Type: protein
Length: 286 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thrombin light chain; Thrombin heavy chain; Hirudin variant-1
EC: 3.4.21.5
UniProt: P00734, P01050
Ligands: M4Z, NAG, NA
Pockets: 3 · best druggability 0.52

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Thrombin light chain (EC 3.4.21.5)	protein	27	37% helix, 0% strand	P00734
B	Thrombin heavy chain (EC 3.4.21.5)	protein	249	14% helix, 36% strand	P00734
D	Hirudin variant-1	protein	10	30% helix, 0% strand	P01050

Ligands and binding sites

M4Z · (2S)-N-[(4-carbamimidoylphenyl)methyl]-1-[(2R)-2-cyclohexyl-2-[[2-(ethylamino)-2-oxidanylidene-ethyl]amino]ethanoyl]azetidine-2-carboxamide · ligand · chains B
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
NA · Sodium ion · metal · 2 copies · chains B

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

Pockets

3 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	140	0.52	0.80	23	M4Z
2	69	0.37	0.78	17	empty
3	77	0.32	0.74	21	empty

Interfaces

2 interfaces between chains.

A–B · 1114 Å² buried · 26 hydrogen bonds · protein-protein
B–D · 658 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 1 glycan, 1 modified (disulfide, N-glycosylation, sulfation).

Compared structures

4BAQ · Thrombin in complex with inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
P01050 · AlphaFold monomer V2.0 prediction for hirudin variant-1 (P01050) · a predicted model of the same protein · chain D against A, TM-score 0.57

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 P01050
Elsewhere: RCSB PDB 4BAQ · PDBe 4BAQ · UniProt P00734 · UniProt P01050

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