MolNFT v1 · #144932 · protein

Human MTR4 helicase in complex with ZCCHC8-ctd

6C90 · Exosome RNA helicase MTR4,EXOSOME RNA helicase MTR4: “Human MTR4 helicase in complex with ZCCHC8-ctd”. X-ray diffraction, 2 ligands (ADP, MG), 6 pockets (best druggability 0.84). MolNFT v1 #144932 on GenesisL1: 3D structure, binding…

PDB: 6C90
Type: protein
Length: 736 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Exosome RNA helicase MTR4,EXOSOME RNA helicase MTR4; Zinc finger cchc domain-containing…
EC: 3.6.4.13
UniProt: P42285, Q6NZY4
Ligands: ADP, MG
Pockets: 6 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 46% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Exosome RNA helicase MTR4,EXOSOME RNA helicase MTR4 (EC 3.6.4.13)	protein	694	47% helix, 14% strand	P42285
B	Zinc finger cchc domain-containing protein 8	protein	42	38% helix, 2% strand	Q6NZY4

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · chains A
MG · Magnesium ion · metal · 2 copies · chains A
MLI · Malonate ion · additive · 4 copies · chains A
TLA · L(+)-tartaric acid · additive · chains A

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

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	906	0.84	0.86	120	MLI
2	598	0.72	0.80	53	ADP
3	184	0.50	0.77	25	empty
4	87	0.40	0.77	20	empty
5	50	0.38	0.81	18	empty

Interfaces

1 interface between chains.

A–B · 2331 Å² buried · 26 hydrogen bonds · protein-protein

Compared structures

6C90 · Human Mtr4 helicase in complex with ZCCHC8-CTD · the same entry in another collection · chain A against A, TM-score 1.00
P42285 · AlphaFold monomer V2.0 prediction for exosome RNA helicase MTR4 (P42285) · a predicted model of the same protein · chain A against A, TM-score 0.98
Q6NZY4 · AlphaFold monomer V2.0 prediction for zinc finger cchc domain- containing protein 8… · a predicted model of the same protein · chain B against A, TM-score 0.29

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 P42285
Every structure of UniProt Q6NZY4
Elsewhere: RCSB PDB 6C90 · PDBe 6C90 · UniProt P42285 · UniProt Q6NZY4

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