MolNFT v1 · #57379 · protein + DNA

Crystal structure of mafg-DNA complex

3A5T · Transcription factor mafg: “Crystal structure of mafg-DNA complex”. X-ray diffraction, 1 ligand (MG), 3 pockets (best druggability 0.68). MolNFT v1 #57379 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3A5T
Type: protein + DNA
Length: 216 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transcription factor mafg; 5'- D(*CP*TP*GP*AP*TP*GP*AP*GP*TP*CP*AP*GP*CP*AP*C)-3'; 5'…
UniProt: O54790
Ligands: MG
Pockets: 3 · best druggability 0.68

Structure

x-ray diffraction · 4 distinct chains · 65% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Transcription factor mafg	protein	93	58% helix, 0% strand	O54790
B	Transcription factor mafg	protein	93	72% helix, 0% strand	O54790
C	5'- D(CPTPGPAPTPGPAPGPTPCPAPGPCPAP*C)-3'	dna	15	—	—
D	5'- D(GPTPGPCPTPGPAPCPTPCPAPTPCPAP*G)-3'	dna	15	—	—

Ligands and binding sites

MG · Magnesium ion · metal · chains C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 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	332	0.68	0.82	31	empty
2	59	0.33	0.77	13	empty
3	58	0.29	0.75	9	empty

Interfaces

6 interfaces between chains.

A–B · 907 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 660 Å² buried · 66 hydrogen bonds · nucleic-nucleic
B–D · 420 Å² buried · 11 hydrogen bonds · protein-nucleic
A–D · 345 Å² buried · 6 hydrogen bonds · protein-nucleic
A–C · 334 Å² buried · 6 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 6 modified (engineered).

Compared structures

3A5T · Crystal structure of MafG-DNA complex · the same entry in another collection · chain A against A, TM-score 1.00
O54790 · AlphaFold monomer V2.0 prediction for transcription factor mafg (O54790) · a predicted model of the same protein · chain B against A, TM-score 0.93

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 O54790
Elsewhere: RCSB PDB 3A5T · PDBe 3A5T · UniProt O54790

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