Research workbench

RNA ligase rtcb-GMP/MN(2+) complex

Analyse RNA ligase rtcb-GMP/MN(2+) complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4DWQ
Type: protein
Length: 962 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TRNA-splicing ligase rtcb
EC: 6.5.1.-
UniProt: O59245
Ligands: 5GP, POP, MN, PO4
Pockets: 5 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	TRNA-splicing ligase rtcb (EC 6.5.1.-)	protein	481	39% helix, 24% strand	O59245

Ligands and binding sites

5GP · Guanosine-5'-monophosphate · ligand · 2 copies · chains A, B
POP · Pyrophosphate 2- · ligand · chains A
MN · Manganese (II) ion · metal · 2 copies · chains A, B
PO4 · Phosphate ion · ion · 5 copies · chains A, B
MLI · Malonate ion · additive · 3 copies · chains A, B
GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1066	0.79	0.81	97	5GP, MN, GOL, PO4
2	962	0.77	0.80	75	5GP, MN, MLI, PO4, POP
3	144	0.67	0.88	28	empty
4	70	0.30	0.74	18	empty
5	57	0.29	0.74	14	empty

Interfaces

1 interface between chains.

A–B · 1128 Å² buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

4DWQ · RNA ligase RtcB-GMP/Mn(2+) complex · the same entry in another collection · chain A against A, TM-score 1.00
O59245 · AlphaFold monomer V2.0 prediction for RNA-splicing ligase rtcb (O59245) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 O59245
Elsewhere: RCSB PDB 4DWQ · PDBe 4DWQ · UniProt O59245

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