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Complex structure of cca adding enzyme with mini-helix lacking cca

Analyse Complex structure of cca adding enzyme with mini-helix lacking cca in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2DR5
Type: protein + RNA
Length: 469 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TRNA (32-mer); Cca-adding enzyme
EC: 2.7.7.25, 2.7.7.21
UniProt: O28126
Ligands: SO4
Pockets: 6 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 44% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	TRNA (32-mer)	rna	32	—	—
A	Cca-adding enzyme (EC 2.7.7.25, 2.7.7.21)	protein	437	44% helix, 21% strand	O28126

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 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, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	805	0.77	0.81	62	SO4
2	671	0.63	0.74	62	empty
3	583	0.60	0.74	28	SO4
4	356	0.53	0.73	28	empty
5	50	0.31	0.76	13	empty

Interfaces

1 interface between chains.

B–A · 1274 Å² buried · 30 hydrogen bonds · protein-nucleic

Compared structures

2DR5 · Complex structure of CCA adding enzyme with mini-helix lacking CCA · the same entry in another collection · chain B against B, TM-score 1.00
O28126 · AlphaFold monomer V2.0 prediction for cca-adding enzyme (O28126) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 O28126
Elsewhere: RCSB PDB 2DR5 · PDBe 2DR5 · UniProt O28126

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