MolNFT v1 · #45724 · protein + DNA

DNA-archeal MC1 protein complex structure by NMR

2NBJ · Chromosomal protein MC1: “DNA-archeal MC1 protein complex structure by NMR”. Solution nmr, 2 pockets (best druggability 0.65). MolNFT v1 #45724 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2NBJ
Type: protein + DNA
Length: 123 residues
Chains: 3
Method: solution nmr
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chromosomal protein MC1; DNA (5'-D(*AP*AP*AP*AP*AP*CP*AP*CP*AP*CP*AP*CP*CP*CP*A)- 3')…
UniProt: A0A0E3KRH5
Pockets: 2 · best druggability 0.65

Structure

solution nmr · 3 distinct chains · 12% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Chromosomal protein MC1	protein	93	12% helix, 44% strand	A0A0E3KRH5
B	DNA (5'-D(APAPAPAPAPCPAPCPAPCPAPCPCPCP*A)- 3')	dna	15	—	—
C	DNA (5'-D(PTPGPGPGPTPGPTPGPTPGPTPTPTPTP*T)- 3')	dna	15	—	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	432	0.65	0.78	32	empty
2	118	0.45	0.78	17	empty

Interfaces

3 interfaces between chains.

B–C · 924 Å² buried · 76 hydrogen bonds · nucleic-nucleic
A–C · 855 Å² buried · 22 hydrogen bonds · protein-nucleic
A–B · 486 Å² buried · 13 hydrogen bonds · protein-nucleic

Compared structures

2NBJ · DNA-archeal MC1 protein complex structure by NMR · the same entry in another collection · chain A against A, TM-score 1.00

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 A0A0E3KRH5
Elsewhere: RCSB PDB 2NBJ · PDBe 2NBJ · UniProt A0A0E3KRH5

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