MolNFT v1 · #180857 · protein + RNA

Polynucleotide phosphorylase

7LD5 · Polyribonucleotide nucleotidyltransferase: “Polynucleotide phosphorylase”. Electron microscopy, 1 ligand (MG), 15 pockets (best druggability 0.85). MolNFT v1 #180857 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7LD5
Type: protein + RNA
Length: 1,773 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Polyribonucleotide nucleotidyltransferase; Poly-a RNA fragment
EC: 2.7.7.8
UniProt: A0QVQ5
Ligands: MG
Pockets: 15 · best druggability 0.85

Structure

electron microscopy · 2 distinct chains · 33% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Polyribonucleotide nucleotidyltransferase (EC 2.7.7.8)	protein	587	33% helix, 27% strand	A0QVQ5
D, E, F	Poly-a RNA fragment	rna	4	—	—

Ligands and binding sites

MG · Magnesium ion · metal · 6 copies · chains A, B, C

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

Pockets

15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	840	0.85	0.88	106	MG
2	479	0.82	0.90	74	empty
3	293	0.78	0.90	37	empty
4	145	0.70	0.90	27	empty
5	148	0.68	0.89	33	empty

Interfaces

9 interfaces between chains.

B–C · 1785 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 1776 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 1766 Å² buried · 12 hydrogen bonds · protein-protein
B–E · 440 Å² buried · 4 hydrogen bonds · protein-nucleic
C–F · 435 Å² buried · 4 hydrogen bonds · protein-nucleic

Compared structures

7LD5 · polynucleotide phosphorylase · the same entry in another collection · chain C against C, TM-score 1.00
A0QVQ5 · AlphaFold monomer V2.0 prediction for polyribonucleotide nucleotidyltransferase (A0QVQ5) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 A0QVQ5
Elsewhere: RCSB PDB 7LD5 · PDBe 7LD5 · UniProt A0QVQ5

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