MolNFT v1 · #124605 · protein + DNA

Structure of PNOB8 aspa-DNA complex.

5KK1: “Structure of PNOB8 aspa-DNA complex.”. X-ray diffraction, 11 pockets (best druggability 0.64). MolNFT v1 #124605 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5KK1
Type: protein + DNA
Length: 607 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aspa; DNA (31-mer)
UniProt: O93706
Pockets: 11 · best druggability 0.64

Structure

x-ray diffraction · 5 distinct chains · 56% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, D, E	Aspa	protein	91	54% helix, 16% strand	O93706
A	Aspa	protein	88	57% helix, 13% strand	O93706
B, F	Aspa	protein	92	59% helix, 16% strand	O93706
P	DNA (31-mer)	dna	31	—	—
N	DNA (31-mer)	dna	31	—	—

Pockets

11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	249	0.64	0.83	35	empty
2	499	0.63	0.76	46	empty
3	356	0.60	0.77	35	empty
4	149	0.49	0.79	21	empty
5	55	0.47	0.85	16	empty

Interfaces

21 interfaces between chains.

E–F · 1623 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 1581 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 1475 Å² buried · 10 hydrogen bonds · protein-protein
P–N · 1328 Å² buried · 116 hydrogen bonds · nucleic-nucleic
B–N · 578 Å² buried · 14 hydrogen bonds · protein-nucleic

Compared structures

5KK1 · 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 5KK1 · PDBe 5KK1 · UniProt O93706

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