MolNFT v1 · #1323 · protein

Thrombin inhibitor from theonalla, cyclotheanamide-based macrocyclic tripeptide motif

1AY6 · Thrombin light chain: “Thrombin inhibitor from theonalla, cyclotheanamide-based macrocyclic tripeptide motif”. X-ray diffraction, 1 ligand (1ZV), 2 pockets (best druggability 0.56). MolNFT v1 #1323 on GenesisL1: 3D structure…

PDB: 1AY6
Type: protein
Length: 291 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thrombin light chain; Thrombin heavy chain; Hirugen
EC: 3.4.21.5
UniProt: P00734, P01050
Ligands: 1ZV
Pockets: 2 · best druggability 0.56

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Thrombin light chain (EC 3.4.21.5)	protein	29	31% helix, 0% strand	P00734
H	Thrombin heavy chain (EC 3.4.21.5)	protein	252	15% helix, 35% strand	P00734
I	Hirugen	protein	10	30% helix, 0% strand	P01050

Ligands and binding sites

1ZV · amino({3-[(3R,5R,14S,16S,21aR)-5,14-dihydroxy-1,4,17-trioxo-16-(2-phenylethyl)icosahydro-1H-pyrrolo[1,2-d][1,4,7,11]tetraazacyclononadecin-3-yl]propyl}amino)methaniminium · ligand · 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	294	0.56	0.76	41	1ZV
2	59	0.30	0.75	13	empty

Interfaces

2 interfaces between chains.

L–H · 1223 Å² buried · 29 hydrogen bonds · protein-protein
H–I · 605 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

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

Compared structures

1AY6 · Thrombin inhibitor from theonalla, cyclotheanamide-based macrocyclic tripeptide motif · the same entry in another collection · chain L against L, TM-score 1.00
P00734 · AlphaFold monomer V2.0 prediction for prothrombin (P00734) · a predicted model of the same protein · chain H against A, TM-score 0.92
P01050 · AlphaFold monomer V2.0 prediction for hirudin variant-1 (P01050) · a predicted model of the same protein · chain I against A, TM-score 0.56

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 1AY6 · PDBe 1AY6 · UniProt P00734 · UniProt P01050

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