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Human exog-H140A in complex with RNA/DNA hybrid duplex

Analyse Human exog-H140A in complex with RNA/DNA hybrid duplex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5ZKJ
Type: protein + DNA + RNA
Length: 648 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nuclease exog, mitochondrial; RNA (5'-R(P*CP*GP*GP*GP*AP*UP*GP*UP*CP*AP*CP*G)-3'); DNA…
EC: 3.1.30.-
UniProt: Q9Y2C4
Ligands: MG, CL
Pockets: 6 · best druggability 0.82

Structure

x-ray diffraction · 4 distinct chains · 33% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nuclease exog, mitochondrial (EC 3.1.30.-)	protein	297	30% helix, 25% strand	Q9Y2C4
B	Nuclease exog, mitochondrial (EC 3.1.30.-)	protein	303	36% helix, 25% strand	Q9Y2C4
C, E	RNA (5'-R(PCPGPGPGPAPUPGPUPCPAPCPG)-3')	rna	12	—	—
D, F	DNA (5'-D(CPGPTPGPAPCPAPTPCPCPCPG)-3')	dna	12	—	—

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A, E, B, C
CL · Chloride ion · ion · chains 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	364	0.82	0.91	65	empty
2	1121	0.80	0.82	68	empty
3	1090	0.79	0.81	66	empty
4	262	0.51	0.75	28	empty
5	184	0.45	0.74	25	empty

Interfaces

7 interfaces between chains.

A–B · 2709 Å² buried · 31 hydrogen bonds · protein-protein
A–E · 707 Å² buried · 27 hydrogen bonds · protein-nucleic
B–C · 700 Å² buried · 34 hydrogen bonds · protein-nucleic
C–D · 605 Å² buried · 52 hydrogen bonds · nucleic-nucleic
E–F · 598 Å² buried · 46 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

5ZKJ · Human EXOG-H140A in complex with RNA/DNA hybrid duplex · the same entry in another collection · chain F against F, TM-score 1.00
Q9Y2C4 · AlphaFold monomer V2.0 prediction for nuclease exog, mitochondrial (Q9Y2C4) · 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 Q9Y2C4
Elsewhere: RCSB PDB 5ZKJ · PDBe 5ZKJ · UniProt Q9Y2C4

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