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Structure of transcriptional regulatory repressor protein - ethr from mycobacterium tuberculosis in complex with sutezolid

Analyse Structure of transcriptional regulatory repressor protein - ethr from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5NZ1
Type: protein
Length: 1,522 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hth-type transcriptional regulator ethr
UniProt: P9WMC1
Ligands: 9EN
Pockets: 17 · best druggability 0.86

Structure

x-ray diffraction · 6 distinct chains · 73% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hth-type transcriptional regulator ethr	protein	191	76% helix, 0% strand	P9WMC1
B	Hth-type transcriptional regulator ethr	protein	193	74% helix, 0% strand	P9WMC1
C	Hth-type transcriptional regulator ethr	protein	189	77% helix, 0% strand	P9WMC1
D, E, F	Hth-type transcriptional regulator ethr	protein	193	72% helix, 0% strand	P9WMC1
G	Hth-type transcriptional regulator ethr	protein	192	69% helix, 0% strand	P9WMC1
H	Hth-type transcriptional regulator ethr	protein	178	71% helix, 0% strand	P9WMC1

Ligands and binding sites

9EN · ~{N}-[[(5~{S})-3-(3-fluoranyl-4-thiomorpholin-4-yl-phenyl)-2-oxidanylidene-1,3-oxazolidin-5-yl]methyl]ethanamide · ligand · 3 copies · chains A, C, D

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

Pockets

17 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1085	0.86	0.87	109	9EN
2	633	0.77	0.83	68	empty
3	672	0.77	0.82	75	9EN
4	624	0.74	0.81	49	empty
5	66	0.72	0.96	19	empty

Interfaces

9 interfaces between chains.

A–B · 1427 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 1401 Å² buried · 12 hydrogen bonds · protein-protein
E–F · 1387 Å² buried · 12 hydrogen bonds · protein-protein
G–H · 1324 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 471 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5NZ1 · Structure of Transcriptional Regulatory Repressor Protein - EthR from Mycobacterium… · the same entry in another collection · chain H against H, TM-score 1.00
P9WMC1 · AlphaFold monomer V2.0 prediction for hth-type transcriptional regulator ethr (P9WMC1) · a predicted model of the same protein · chain A against A, TM-score 0.99

Analyse

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Every structure of UniProt P9WMC1
Elsewhere: RCSB PDB 5NZ1 · PDBe 5NZ1 · UniProt P9WMC1

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