MolNFT v1 · #95515 · protein

RNA ligase rtcb in complex with MN(II)

4ISJ · TRNA-splicing ligase rtcb: “RNA ligase rtcb in complex with MN(II)”. X-ray diffraction, 4 ligands (GLC, FRU, MN), 4 pockets (best druggability 0.79). MolNFT v1 #95515 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4ISJ
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: GLC, FRU, MN, SO4
Pockets: 4 · 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.-, 3.1.-.-)	protein	480	39% helix, 24% strand	O59245

Ligands and binding sites

GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, B
FRU · beta-D-fructofuranose · sugar · 2 copies · chains A, B
MN · Manganese (II) ion · metal · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 13 copies · chains A, B

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

Pockets

4 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	1130	0.79	0.81	105	SO4
2	986	0.76	0.79	77	SO4
3	111	0.60	0.87	23	empty
4	78	0.30	0.72	22	empty

Interfaces

1 interface between chains.

A–B · 1150 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

4ISJ · RNA Ligase RtcB in complex with 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 4ISJ · PDBe 4ISJ · UniProt O59245

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