MolNFT v1 · #20234 · protein + DNA

Crystal structure of mtan bound to DNA

1R8D · 26-mer: “Crystal structure of mtan bound to DNA”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.48). MolNFT v1 #20234 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1R8D
Type: protein + DNA
Length: 268 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 26-mer; Transcription activator mtan
UniProt: P71039
Ligands: SO4
Pockets: 4 · best druggability 0.48

Structure

x-ray diffraction · 4 distinct chains · 64% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	26-mer	dna	26	—	—
D	26-mer	dna	26	—	—
A	Transcription activator mtan	protein	109	65% helix, 6% strand	P71039
B	Transcription activator mtan	protein	107	63% helix, 6% strand	P71039

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains C, D, A, B

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

Pockets

4 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	231	0.48	0.74	30	SO4
2	135	0.43	0.76	19	SO4
3	63	0.34	0.77	13	empty
4	50	0.23	0.72	11	SO4

Interfaces

6 interfaces between chains.

C–D · 1047 Å² buried · 94 hydrogen bonds · nucleic-nucleic
A–B · 1004 Å² buried · 5 hydrogen bonds · protein-protein
C–B · 514 Å² buried · 10 hydrogen bonds · protein-nucleic
D–A · 492 Å² buried · 9 hydrogen bonds · protein-nucleic
C–A · 375 Å² buried · 9 hydrogen bonds · protein-nucleic

Compared structures

1R8D · Crystal Structure of MtaN Bound to DNA · the same entry in another collection · chain C against C, TM-score 1.00
P71039 · AlphaFold monomer V2.0 prediction for hth-type transcriptional activator mta (P71039) · a predicted model of the same protein · chain B against A, TM-score 0.69

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 P71039
Elsewhere: RCSB PDB 1R8D · PDBe 1R8D · UniProt P71039

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