Research workbench

RNA ligase rtcb in complex with GTP alphas and MN(II)

Analyse RNA ligase rtcb in complex with GTP alphas and MN(II) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4ISZ
Type: protein
Length: 960 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TRNA-splicing ligase rtcb
EC: 6.5.1.-, 3.1.-.-
UniProt: O59245
Ligands: GAV, GLC, FRU, MN, SO4
Pockets: 6 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	TRNA-splicing ligase rtcb (EC 6.5.1.-, 3.1.-.-)	protein	480	38% helix, 25% strand	O59245

Ligands and binding sites

GAV · Guanosine-5'-rp-alpha-thio-triphosphate · ligand · 2 copies · chains A, B
GLC · alpha-D-glucopyranose · sugar · 3 copies · chains A, B
FRU · beta-D-fructofuranose · sugar · 3 copies · chains A, B
MN · Manganese (II) ion · metal · 4 copies · chains A, B
SO4 · Sulfate ion · ion · 18 copies · chains A, B

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

Pockets

6 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	SO4, GAV, MN
2	996	0.77	0.79	74	GAV, MN, SO4
3	123	0.63	0.87	25	empty
4	52	0.29	0.76	12	empty
5	50	0.25	0.73	15	empty

Interfaces

1 interface between chains.

A–B · 1189 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

4ISZ · RNA ligase RtcB in complex with GTP alphaS and Mn(II) · 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 4ISZ · PDBe 4ISZ · UniProt O59245

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