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Structure of endoms-DSDNA1' complex

Analyse Structure of endoms-DSDNA1' complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5GKF
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*CP*TP*AP*CP*AP*TP*GP*TP*CP*GP*TP*CP*C)- 3'); DNA…
EC: 3.1.-.-
UniProt: Q5JER9
Ligands: MG
Pockets: 6 · best druggability 0.84

Structure

x-ray diffraction · 3 distinct chains · 24% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Endonuclease endoms (EC 3.1.-.-)	protein	239	24% helix, 45% strand	Q5JER9
C	DNA (5'-D(CPGPCPTPAPCPAPTPGPTPCPGPTPCP*C)- 3')	dna	15	—	—
D	DNA (5'-D(GPGPAPCPGPAPCPTPTPGPTPAPGPCP*G)- 3')	dna	15	—	—

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A, D, B, C
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

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	368	0.84	0.94	37	empty
2	542	0.71	0.80	41	MPD
3	631	0.71	0.79	47	MPD
4	500	0.64	0.77	27	empty
5	441	0.58	0.75	28	empty

Interfaces

6 interfaces between chains.

A–B · 3125 Å² buried · 59 hydrogen bonds · protein-protein
A–D · 678 Å² buried · 13 hydrogen bonds · protein-nucleic
B–C · 662 Å² buried · 12 hydrogen bonds · protein-nucleic
A–C · 653 Å² buried · 19 hydrogen bonds · protein-nucleic
C–D · 640 Å² buried · 53 hydrogen bonds · nucleic-nucleic

Compared structures

5GKF · Structure of EndoMS-dsDNA1' 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 5GKF · PDBe 5GKF · UniProt Q5JER9

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