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Cryoem structure of DNA-pk complex VIII

Analyse Cryoem structure of DNA-pk complex VIII in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7SUD
Type: protein
Length: 3,749 residues
Chains: 2
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA-dependent protein kinase catalytic subunit; X-ray repair cross-complementing protein 5
EC: 2.7.11.1, 3.6.4.-
UniProt: P78527, P13010
Ligands: ATP, MG
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 2 distinct chains · 59% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-dependent protein kinase catalytic subunit (EC 2.7.11.1)	protein	3740	59% helix, 2% strand	P78527
C	X-ray repair cross-complementing protein 5 (EC 3.6.4.-)	protein	9	44% helix, 0% strand	P13010

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · chains A
MG · Magnesium ion · metal · chains A

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	928	0.85	0.87	117	MG, ATP
2	826	0.80	0.83	94	empty
3	358	0.80	0.89	62	empty
4	378	0.79	0.89	56	empty
5	75	0.75	0.98	18	empty

Interfaces

1 interface between chains.

A–C · 402 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 4 modified (phosphorylation).

Compared structures

7SUD · CryoEM structure of DNA-PK complex VIII · the same entry in another collection · chain C against C, TM-score 1.00
P13010 · AlphaFold monomer V2.0 prediction for X-ray repair cross- complementing protein 5 (P13010) · a predicted model of the same protein · chain C against A, TM-score 0.68

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 P78527
Every structure of UniProt P13010
Elsewhere: RCSB PDB 7SUD · PDBe 7SUD · UniProt P78527 · UniProt P13010

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