MolNFT v1 · #95532 · protein

Structure of the RNA ligase rtcb-GMP/MN(II) complex

4IT0 · TRNA-splicing ligase rtcb: “Structure of the RNA ligase rtcb-GMP/MN(II) complex”. X-ray diffraction, 5 ligands (5GP, GLC, FRU), 5 pockets (best druggability 0.79). MolNFT v1 #95532 on GenesisL1: 3D structure, binding sites and…

PDB: 4IT0
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: 5GP, GLC, FRU, MN, SO4
Pockets: 5 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 26% 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, 26% strand	O59245

Ligands and binding sites

5GP · Guanosine-5'-monophosphate · ligand · chains A
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 · 4 copies · chains A, B
SO4 · Sulfate ion · ion · 19 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	1053	0.79	0.81	94	SO4
2	879	0.75	0.79	71	MN, 5GP, SO4
3	80	0.67	0.93	23	empty
4	57	0.28	0.74	12	empty
5	56	0.27	0.73	15	empty

Interfaces

1 interface between chains.

A–B · 1240 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

4IT0 · Structure of the RNA ligase RtcB-GMP/Mn(II) 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 4IT0 · PDBe 4IT0 · UniProt O59245

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