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Human thrombin-inhibitor complex

Analyse Human thrombin-inhibitor complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1K21
Type: protein
Length: 286 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Prothrombin; Hirudin variant-2
EC: 3.4.21.5
UniProt: P00734, P09945
Ligands: IGN, NAG, NA
Pockets: 4 · best druggability 0.54

Structure

x-ray diffraction · 3 distinct chains · 17% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Prothrombin (EC 3.4.21.5)	protein	27	37% helix, 0% strand	P00734
H	Prothrombin (EC 3.4.21.5)	protein	249	14% helix, 35% strand	P00734
I	Hirudin variant-2	protein	10	30% helix, 0% strand	P09945

Ligands and binding sites

IGN · {[(1R)-2-((2S)-2-{[(3-{[amino(imino)methyl]amino}propyl)amino]carbonyl}piperidinyl)-1-(cyclohexylmethyl)-2-oxoethyl]amino}acetic acid · ligand · chains H
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains H
NA · Sodium ion · metal · 2 copies · chains H

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 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	223	0.54	0.78	40	IGN
2	78	0.35	0.76	17	empty
3	55	0.29	0.75	11	empty
4	50	0.28	0.75	16	empty

Interfaces

2 interfaces between chains.

L–H · 1103 Å² buried · 26 hydrogen bonds · protein-protein
H–I · 671 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide, 1 glycan, 1 modified (disulfide, N-glycosylation, sulfation).

Compared structures

1K21 · Human thrombin-inhibitor complex · the same entry in another collection · chain L against L, TM-score 1.00
P09945 · AlphaFold monomer V2.0 prediction for hirudin variant-2 (P09945) · 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 P09945
Elsewhere: RCSB PDB 1K21 · PDBe 1K21 · UniProt P00734 · UniProt P09945

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