MolNFT v1 · #123998 · protein + DNA

P2(1) structure of PNOB8 aspa-DNA complex

5K1Y: “P2(1) structure of PNOB8 aspa-DNA complex”. X-ray diffraction, 10 pockets (best druggability 0.70). MolNFT v1 #123998 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5K1Y
Type: protein + DNA
Length: 611 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aspa; DNA (33-mer)
UniProt: O93706
Pockets: 10 · best druggability 0.70

Structure

x-ray diffraction · 5 distinct chains · 56% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, E	Aspa	protein	91	54% helix, 9% strand	O93706
D, B, F	Aspa	protein	92	58% helix, 13% strand	O93706
A	Aspa	protein	87	57% helix, 6% strand	O93706
P	DNA (33-mer)	dna	33	—	—
N	DNA (33-mer)	dna	33	—	—

Pockets

10 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	371	0.70	0.83	37	empty
2	406	0.66	0.79	34	empty
3	390	0.65	0.80	32	empty
4	382	0.63	0.78	33	empty
5	107	0.45	0.79	17	empty

Interfaces

21 interfaces between chains.

C–D · 1654 Å² buried · 11 hydrogen bonds · protein-protein
E–F · 1541 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1488 Å² buried · 9 hydrogen bonds · protein-protein
P–N · 1427 Å² buried · 127 hydrogen bonds · nucleic-nucleic
B–P · 546 Å² buried · 6 hydrogen bonds · protein-nucleic

Compared structures

5K1Y · P2(1) Structure of pNOB8 AspA-DNA complex · the same entry in another collection · chain C against C, 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 O93706
Elsewhere: RCSB PDB 5K1Y · PDBe 5K1Y · UniProt O93706

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