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MolNFT v1 · #27516 · protein

Nonbasic thrombin inhibitor complex

1XM1: “Nonbasic thrombin inhibitor complex”. X-ray diffraction, 1 ligand (GAH), 1 pocket (best druggability 0.60). MolNFT v1 #27516 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
1XM1
Type
protein
Length
294 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Thrombin; Hirudin
EC
3.4.21.5
UniProt
P00734, P28504
Ligands
GAH
Pockets
1 · best druggability 0.60

Structure

x-ray diffraction · 2 distinct chains · 18% helix, 30% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AThrombin (EC 3.4.21.5)protein28417% helix, 31% strandP00734
HHirudinprotein1030% helix, 0% strandP28504

Ligands and binding sites

  • GAH · N-{[(2S)-1-(N-{[4-({[amino(imino)methyl]amino}methyl)cyclohexyl]carbonyl}-3-cyclohexyl-L-alanyl)azetidin-2-yl]carbonyl}-L-tyrosyl-N~6~-[amino(imino)methyl]-L-lysinamide · ligand · chains A

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.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
13360.600.7742GAH

Interfaces

1 interface between chains.

  • A–H · 690 Ų buried · 7 hydrogen bonds · protein-protein

Modifications

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

Compared structures

  • 1XM1 · Nonbasic Thrombin Inhibitor Complex · 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 H against A, TM-score 0.56

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