MolNFT v1 · #160113 · protein + DNA

Crystal structure of the human pax-6 paired domain-DNA complex reveals a general model for pax protein-DNA interactions

6PAX · 26 nucleotide DNA: “Crystal structure of the human pax-6 paired domain-DNA complex reveals a general model for pax protein-DNA…”. X-ray diffraction, 3 pockets (best druggability 0.39). MolNFT v1 #160113 on GenesisL1: 3D structure…

PDB: 6PAX
Type: protein + DNA
Length: 185 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 26 nucleotide DNA; Homeobox protein pax-6
UniProt: P26367
Pockets: 3 · best druggability 0.39

Structure

x-ray diffraction · 3 distinct chains · 53% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	26 nucleotide DNA	dna	26	—	—
C	26 nucleotide DNA	dna	26	—	—
A	Homeobox protein pax-6	protein	133	53% helix, 5% strand	P26367

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	114	0.39	0.75	20	empty
2	115	0.38	0.75	20	empty
3	72	0.30	0.74	15	empty

Interfaces

3 interfaces between chains.

B–C · 1098 Å² buried · 106 hydrogen bonds · nucleic-nucleic
C–A · 1023 Å² buried · 20 hydrogen bonds · protein-nucleic
B–A · 981 Å² buried · 30 hydrogen bonds · protein-nucleic

Compared structures

6PAX · Crystal structure of the human pax-6 paired domain-DNA complex reveals a general model… · the same entry in another collection · chain B against B, TM-score 1.00
P26367 · AlphaFold monomer V2.0 prediction for paired box protein pax-6 (P26367) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P26367
Elsewhere: RCSB PDB 6PAX · PDBe 6PAX · UniProt P26367

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