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Crystal structure of a rex-family REPRESSOR/DNA/NAD+ complex from thermus aquaticus

Analyse Crystal structure of a rex-family REPRESSOR/DNA/NAD+ complex from thermus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3IKT
Type: protein + DNA
Length: 454 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Redox-sensing transcriptional repressor rex; Rex operator DNA
UniProt: Q72I39
Ligands: NAD
Pockets: 5 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 42% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Redox-sensing transcriptional repressor rex	protein	204	43% helix, 18% strand	Q72I39
B	Redox-sensing transcriptional repressor rex	protein	206	41% helix, 18% strand	Q72I39
C, D	Rex operator DNA	dna	22	—	—

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A, B

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	931	0.78	0.80	99	NAD
2	970	0.75	0.78	94	empty
3	99	0.36	0.74	13	empty
4	69	0.35	0.77	12	empty
5	55	0.29	0.76	13	empty

Interfaces

6 interfaces between chains.

A–B · 2682 Å² buried · 27 hydrogen bonds · protein-protein
C–D · 1041 Å² buried · 106 hydrogen bonds · nucleic-nucleic
B–D · 519 Å² buried · 12 hydrogen bonds · protein-nucleic
B–C · 504 Å² buried · 3 hydrogen bonds · protein-nucleic
A–C · 436 Å² buried · 9 hydrogen bonds · protein-nucleic

Compared structures

3IKT · Crystal structure of a Rex-family repressor/DNA/NAD+ complex from Thermus aquaticus · the same entry in another collection · chain A against A, TM-score 1.00
Q72I39 · AlphaFold monomer V2.0 prediction for redox-sensing transcriptional repressor rex (Q72I39) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 Q72I39
Elsewhere: RCSB PDB 3IKT · PDBe 3IKT · UniProt Q72I39

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