MolNFT v1 · #89690 · protein

RNA ligase RTCB/MN2+ complex

4DWR · TRNA-splicing ligase rtcb: “RNA ligase RTCB/MN2+ complex”. X-ray diffraction, 4 ligands (GLC, FRU, MN), 7 pockets (best druggability 0.64). MolNFT v1 #89690 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4DWR
Type: protein
Length: 1,450 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TRNA-splicing ligase rtcb
EC: 6.5.1.-
UniProt: O59245
Ligands: GLC, FRU, MN, SO4
Pockets: 7 · best druggability 0.64

Structure

x-ray diffraction · 3 distinct chains · 38% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	TRNA-splicing ligase rtcb (EC 6.5.1.-)	protein	486	37% helix, 23% strand	O59245
A	TRNA-splicing ligase rtcb (EC 6.5.1.-)	protein	483	38% helix, 24% strand	O59245
C	TRNA-splicing ligase rtcb (EC 6.5.1.-)	protein	481	38% helix, 24% strand	O59245

Ligands and binding sites

GLC · alpha-D-glucopyranose · sugar · 3 copies · chains B, A, C
FRU · beta-D-fructofuranose · sugar · 3 copies · chains B, A, C
MN · Manganese (II) ion · metal · 6 copies · chains B, A, C
SO4 · Sulfate ion · ion · 21 copies · chains B, A, C

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

Pockets

7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	309	0.64	0.80	45	empty
2	463	0.64	0.78	47	MN, SO4
3	318	0.62	0.79	37	MN, SO4
4	321	0.62	0.79	22	GLC, FRU
5	346	0.60	0.77	41	MN, SO4

Interfaces

2 interfaces between chains.

B–A · 751 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 564 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

4DWR · RNA ligase RtcB/Mn2+ complex · the same entry in another collection · chain B against B, 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 0.97

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 4DWR · PDBe 4DWR · UniProt O59245

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