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X-ray structure of the complex between human alpha thrombin and a modified thrombin binding aptamer (mtba)

Analyse X-ray structure of the complex between human alpha thrombin and a modified… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3QLP
Type: protein + DNA
Length: 308 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thrombin heavy chain; Thrombin light chain; Modified thrombin binding DNA aptamer
EC: 3.4.21.5
UniProt: P00734
Ligands: 0G6, NAG, NA, K
Pockets: 2 · best druggability 0.56

Structure

x-ray diffraction · 3 distinct chains · 16% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Thrombin heavy chain (EC 3.4.21.5)	protein	259	14% helix, 34% strand	P00734
L	Thrombin light chain (EC 3.4.21.5)	protein	34	29% helix, 0% strand	P00734
D	Modified thrombin binding DNA aptamer	dna	15	—	—

Ligands and binding sites

0G6 · D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide · ligand · chains H
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains H
NA · Sodium ion · metal · chains H
K · Potassium ion · metal · chains D

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	240	0.56	0.78	37	0G6
2	55	0.34	0.78	19	empty

Interfaces

2 interfaces between chains.

H–L · 1465 Å² buried · 38 hydrogen bonds · protein-protein
H–D · 685 Å² buried · 22 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 4 disulfide, 2 covalent, 1 glycan (disulfide, covalent ligand, N-glycosylation).

Compared structures

3QLP · X-ray structure of the complex between human alpha thrombin and a modified thrombin… · the same entry in another collection · chain H against H, 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 0.91

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
Elsewhere: RCSB PDB 3QLP · PDBe 3QLP · UniProt P00734

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