Research workbench

Exploring thrombin S1 pocket

Analyse Exploring thrombin S1 pocket in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2ZDV
Type: protein
Length: 289 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: 37U, NA, PO4
Pockets: 2 · best druggability 0.56

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Thrombin light chain (EC 3.4.21.5)	protein	28	36% helix, 0% strand	P00734
H	Thrombin heavy chain (EC 3.4.21.5)	protein	250	15% helix, 36% strand	P00734
I	Hirudin variant-1	protein	11	27% helix, 0% strand	P01050

Ligands and binding sites

37U · D-phenylalanyl-N-(3-fluorobenzyl)-L-prolinamide · ligand · chains H
NA · Sodium ion · metal · 2 copies · chains H
PO4 · Phosphate ion · ion · 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	286	0.56	0.76	40	37U
2	59	0.30	0.75	13	empty

Interfaces

2 interfaces between chains.

L–H · 1149 Å² buried · 29 hydrogen bonds · protein-protein
H–I · 642 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

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

Compared structures

2ZDV · Exploring Thrombin S1 pocket · the same entry in another collection · chain L against L, TM-score 1.00
P01050 · AlphaFold monomer V2.0 prediction for hirudin variant-1 (P01050) · a predicted model of the same protein · chain I against A, TM-score 0.49

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 2ZDV · PDBe 2ZDV · UniProt P00734 · UniProt P01050

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