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Cryo-EM structure of DNA-PKCS:KU80CT194

Analyse Cryo-EM structure of DNA-PKCS:KU80CT194 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6ZH6
Type: protein
Length: 3,705 residues
Chains: 2
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA-dependent protein kinase catalytic SUBUNIT,DNA-pkcs; X-ray repair cross-complementing…
EC: 2.7.11.1, 3.6.4.-
UniProt: P78527, P13010
Pockets: 20 · best druggability 0.87

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,DNA-pkcs (EC 2.7.11.1)	protein	3692	59% helix, 2% strand	P78527
B	X-ray repair cross-complementing protein 5 (EC 3.6.4.-)	protein	13	77% helix, 0% strand	P13010

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	1041	0.87	0.88	112	empty
2	1145	0.85	0.85	114	empty
3	563	0.84	0.89	84	empty
4	877	0.82	0.84	104	empty
5	952	0.81	0.83	106	empty

Interfaces

1 interface between chains.

A–B · 164 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6ZH6 · Cryo-EM structure of DNA-PKcs:Ku80ct194 · the same entry in another collection · chain B against B, 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 B against A, TM-score 0.60

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 6ZH6 · PDBe 6ZH6 · UniProt P78527 · UniProt P13010

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