MolNFT v1 · #48160 · protein

Thrombin in complex with inhibitor

2PKS · Thrombin light chain: “Thrombin in complex with inhibitor”. X-ray diffraction, 2 ligands (G44, NA), 3 pockets (best druggability 0.53). MolNFT v1 #48160 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2PKS
Type: protein
Length: 286 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thrombin light chain; Thrombin heavy chain fragment; Hirudin
UniProt: P00734, P28504
Ligands: G44, NA
Pockets: 3 · best druggability 0.53

Structure

x-ray diffraction · 4 distinct chains · 16% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Thrombin light chain	protein	27	33% helix, 0% strand	P00734
B	Thrombin heavy chain fragment	protein	147	11% helix, 37% strand	P00734
C	Thrombin heavy chain fragment	protein	102	17% helix, 32% strand	P00734
D	Hirudin	protein	10	30% helix, 0% strand	P28504

Ligands and binding sites

G44 · 4-({[4-(3-methylbenzoyl)pyridin-2-yl]amino}methyl)benzenecarboximidamide · ligand · chains B, C
NA · Sodium ion · metal · chains C

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	230	0.53	0.77	34	G44
2	76	0.37	0.77	20	empty
3	58	0.31	0.76	18	empty

Interfaces

5 interfaces between chains.

B–C · 3320 Å² buried · 58 hydrogen bonds · protein-protein
A–B · 838 Å² buried · 12 hydrogen bonds · protein-protein
B–D · 637 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 582 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 42 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

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

Compared structures

2PKS · Thrombin in complex with inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
P28504 · AlphaFold monomer V2.0 prediction for hirudin-2 (P28504) · a predicted model of the same protein · chain D against A, TM-score 0.48

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 2PKS · PDBe 2PKS · UniProt P00734 · UniProt P28504

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