MolNFT v1 · #119949 · protein + DNA

Structure of endoms-DSDNA2 complex

5GKH · Endonuclease endoms: “Structure of endoms-DSDNA2 complex”. X-ray diffraction, 1 ligand (MG), 4 pockets (best druggability 0.83). MolNFT v1 #119949 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5GKH
Type: protein + DNA
Length: 508 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Endonuclease endoms; DNA (5'-D(*CP*GP*TP*GP*CP*CP*AP*GP*GP*TP*GP*CP*CP*GP*T)- 3'); DNA…
EC: 3.1.-.-
UniProt: Q5JER9
Ligands: MG
Pockets: 4 · best druggability 0.83

Structure

x-ray diffraction · 3 distinct chains · 23% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Endonuclease endoms (EC 3.1.-.-)	protein	239	23% helix, 44% strand	Q5JER9
C	DNA (5'-D(CPGPTPGPCPCPAPGPGPTPGPCPCPGP*T)- 3')	dna	15	—	—
D	DNA (5'-D(APCPGPGPCPAPCPTPTPGPGPCPAPCP*G)- 3')	dna	15	—	—

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A, C, B, D
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 5 copies · chains A, C, D, B

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

Pockets

4 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	370	0.83	0.92	35	empty
2	1075	0.79	0.81	84	MPD
3	459	0.61	0.76	33	empty
4	400	0.57	0.75	28	empty

Interfaces

6 interfaces between chains.

A–B · 3134 Å² buried · 62 hydrogen bonds · protein-protein
C–D · 650 Å² buried · 77 hydrogen bonds · nucleic-nucleic
B–D · 637 Å² buried · 13 hydrogen bonds · protein-nucleic
A–C · 631 Å² buried · 15 hydrogen bonds · protein-nucleic
A–D · 573 Å² buried · 17 hydrogen bonds · protein-nucleic

Compared structures

5GKH · Structure of EndoMS-dsDNA2 complex · the same entry in another collection · chain A against A, TM-score 1.00
Q5JER9 · AlphaFold monomer V2.0 prediction for endonuclease nucs (Q5JER9) · 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 Q5JER9
Elsewhere: RCSB PDB 5GKH · PDBe 5GKH · UniProt Q5JER9

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