MolNFT v1 · #116777 · protein + RNA

Thrombin-RNA aptamer complex

5DO4 · Thrombin light chain: “Thrombin-RNA aptamer complex”. X-ray diffraction, 4 ligands (0G6, NAG, CA), 6 pockets (best druggability 0.77). MolNFT v1 #116777 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5DO4
Type: protein + RNA
Length: 313 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thrombin light chain; Thrombin heavy chain; RNA (25-mer)
EC: 3.4.21.5
UniProt: P00734
Ligands: 0G6, NAG, CA, MG
Pockets: 6 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 18% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Thrombin light chain (EC 3.4.21.5)	protein	32	31% helix, 0% strand	P00734
H	Thrombin heavy chain (EC 3.4.21.5)	protein	256	16% helix, 35% strand	P00734
A	RNA (25-mer)	rna	25	—	—

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
CA · Calcium ion · metal · chains H
MG · Magnesium ion · metal · chains H, A
EDO · 1,2-ethanediol · additive · 4 copies · chains L, H, A
GOL · Glycerol · additive · 2 copies · chains L, H
MRD · (4R)-2-methylpentane-2,4-diol · additive · chains H, A

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

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	112	0.77	0.96	24	EDO, MRD
2	251	0.56	0.78	41	0G6
3	89	0.46	0.81	16	MG
4	126	0.42	0.76	13	empty
5	93	0.38	0.76	17	GOL

Interfaces

3 interfaces between chains.

L–H · 1241 Å² buried · 31 hydrogen bonds · protein-protein
H–A · 1009 Å² buried · 20 hydrogen bonds · protein-nucleic
L–A · 99 Å² buried · 6 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 11 modified, 4 disulfide, 2 covalent, 1 glycan (nucleotide modification, disulfide, covalent ligand, N-glycosylation).

Compared structures

5DO4 · Thrombin-RNA aptamer complex · the same entry in another collection · chain A against A, 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 5DO4 · PDBe 5DO4 · UniProt P00734

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