MolNFT v1 · #19513 · protein

Crystal structure of RNA 3'-terminal phosphate cyclase, an ubiquitous enzyme with unusual topology

1QMI: “Crystal structure of RNA 3'-terminal phosphate cyclase, an ubiquitous enzyme with unusual topology”. X-ray diffraction, 11 pockets (best druggability 0.80). MolNFT v1 #19513 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 1QMI
Type: protein
Length: 1,340 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA 3'-terminal phosphate cyclase
EC: 6.5.1.4
UniProt: P46849
Pockets: 11 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	RNA 3'-terminal phosphate cyclase (EC 6.5.1.4)	protein	335	34% helix, 28% strand	P46849

Pockets

11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1129	0.80	0.81	102	empty
2	839	0.80	0.83	105	empty
3	874	0.78	0.81	80	empty
4	932	0.77	0.79	84	empty
5	348	0.62	0.78	44	empty

Interfaces

5 interfaces between chains.

C–D · 723 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 629 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 257 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 245 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 93 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 modified, 2 disulfide (engineered, disulfide).

Compared structures

1QMI · Crystal structure of RNA 3'-terminal phosphate cyclase, an ubiquitous enzyme with unusual… · the same entry in another collection · chain A against A, TM-score 1.00
P46849 · AlphaFold monomer V2.0 prediction for RNA 3'-terminal phosphate cyclase (P46849) · 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 P46849
Elsewhere: RCSB PDB 1QMI · PDBe 1QMI · UniProt P46849

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