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Human exog-H140A in complex with duplex DNA

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

PDB: 5ZKI
Type: protein + DNA
Length: 652 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nuclease exog, mitochondrial; DNA (5'-D(*CP*GP*GP*GP*AP*TP*AP*TP*CP*CP*CP*G)-3')
EC: 3.1.30.-
UniProt: Q9Y2C4
Ligands: MG, CL
Pockets: 5 · best druggability 0.83

Structure

x-ray diffraction · 3 distinct chains · 35% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nuclease exog, mitochondrial (EC 3.1.30.-)	protein	300	35% helix, 24% strand	Q9Y2C4
C, D, E, F	DNA (5'-D(CPGPGPGPAPTPAPTPCPCPCPG)-3')	dna	12	—	—
B	Nuclease exog, mitochondrial (EC 3.1.30.-)	protein	304	35% helix, 24% strand	Q9Y2C4

Ligands and binding sites

MG · Magnesium ion · metal · 3 copies · chains A, C, E, B
CL · Chloride ion · ion · 2 copies · chains A, B

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	353	0.83	0.92	64	empty
2	937	0.76	0.79	62	CL
3	953	0.75	0.78	68	CL, MG
4	171	0.44	0.74	21	empty
5	156	0.43	0.74	15	empty

Interfaces

7 interfaces between chains.

A–B · 2678 Å² buried · 34 hydrogen bonds · protein-protein
E–B · 671 Å² buried · 21 hydrogen bonds · protein-nucleic
A–C · 661 Å² buried · 22 hydrogen bonds · protein-nucleic
E–F · 579 Å² buried · 60 hydrogen bonds · nucleic-nucleic
C–D · 570 Å² buried · 56 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

5ZKI · Human EXOG-H140A in complex with duplex DNA · the same entry in another collection · chain B against B, 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 0.99

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 5ZKI · PDBe 5ZKI · UniProt Q9Y2C4

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