MolNFT v1 · #54784 · protein + RNA

UPF1-RNA complex

2XZL · ATP-dependent helicase NAM7: “UPF1-RNA complex”. X-ray diffraction, 4 ligands (ADP, ALF, ZN), 9 pockets (best druggability 0.77). MolNFT v1 #54784 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2XZL
Type: protein + RNA
Length: 764 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATP-dependent helicase NAM7; 5- R(*UP*UP*UP*UP*UP*UP*UP*UP*U) -3
EC: 3.6.4.13
UniProt: P30771
Ligands: ADP, ALF, ZN, MG
Pockets: 9 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 35% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ATP-dependent helicase NAM7 (EC 3.6.4.13)	protein	756	35% helix, 18% strand	P30771
B	5- R(UPUPUPUPUPUPUPUP*U) -3	rna	8	—	—

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · chains A
ALF · Tetrafluoroaluminate ion · ligand · chains A
ZN · Zinc ion · metal · 3 copies · chains A
MG · Magnesium ion · metal · chains A
1PE · Pentaethylene glycol · additive · 12 copies · chains A

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

Pockets

9 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	113	0.77	0.97	26	empty
2	1165	0.75	0.78	125	empty
3	165	0.67	0.87	31	ADP, ALF, MG
4	557	0.62	0.75	38	empty
5	53	0.44	0.83	12	empty

Interfaces

1 interface between chains.

A–B · 1194 Å² buried · 25 hydrogen bonds · protein-nucleic

Compared structures

2XZL · Upf1-RNA complex · the same entry in another collection · chain A against A, TM-score 1.00
P30771 · AlphaFold monomer V2.0 prediction for ATP-dependent helicase NAM7 (P30771) · a predicted model of the same protein · chain A against A, TM-score 0.81

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 P30771
Elsewhere: RCSB PDB 2XZL · PDBe 2XZL · UniProt P30771

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