MolNFT v1 · #52222 · protein

The structure of an archaeal homodimeric RNA ligase

2VUG · PAB1020: “The structure of an archaeal homodimeric RNA ligase”. X-ray diffraction, 1 ligand (ANP), 7 pockets (best druggability 0.72). MolNFT v1 #52222 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2VUG
Type: protein
Length: 746 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: PAB1020
UniProt: Q9UYG2
Ligands: ANP
Pockets: 7 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	PAB1020	protein	373	38% helix, 28% strand	Q9UYG2

Ligands and binding sites

ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 5 copies · chains A, B
MRD · (4R)-2-methylpentane-2,4-diol · additive · 2 copies · chains B

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

Pockets

7 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	858	0.72	0.77	84	ANP, MPD
2	737	0.71	0.77	67	ANP, MPD
3	103	0.40	0.76	18	empty
4	72	0.37	0.77	15	MRD
5	83	0.37	0.76	20	empty

Interfaces

1 interface between chains.

A–B · 2371 Å² buried · 28 hydrogen bonds · protein-protein

Compared structures

2VUG · The structure of an archaeal homodimeric RNA ligase · the same entry in another collection · chain A against A, TM-score 1.00

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 Q9UYG2
Elsewhere: RCSB PDB 2VUG · PDBe 2VUG · UniProt Q9UYG2

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