MolNFT v1 · #48532 · protein

Crystal structure of sulfo-hirudin complexed to thrombin

2PW8 · Thrombin light chain: “Crystal structure of sulfo-hirudin complexed to thrombin”. X-ray diffraction, 2 ligands (NI, NA), 2 pockets (best druggability 0.56). MolNFT v1 #48532 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 2PW8
Type: protein
Length: 340 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
UniProt: P00734, P01050
Ligands: NI, NA
Pockets: 2 · best druggability 0.56

Structure

x-ray diffraction · 3 distinct chains · 16% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Thrombin light chain	protein	27	37% helix, 0% strand	P00734
H	Thrombin heavy chain	protein	251	16% helix, 35% strand	P00734
I	Hirudin variant-1	protein	62	5% helix, 31% strand	P01050

Ligands and binding sites

NI · Nickel (II) ion · metal · chains L, H
NA · Sodium ion · metal · 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	190	0.56	0.80	26	empty
2	81	0.36	0.76	18	empty

Interfaces

2 interfaces between chains.

H–I · 1650 Å² buried · 21 hydrogen bonds · protein-protein
L–H · 1134 Å² buried · 28 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide, 1 modified (disulfide, sulfation).

Compared structures

2PW8 · Crystal structure of sulfo-hirudin complexed to thrombin · 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 0.87

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 2PW8 · PDBe 2PW8 · UniProt P00734 · UniProt P01050

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