MolNFT v1 · #61571 · protein

The crystal structure of a tetr transcription regulator from silicibacter pomeroyi dss

3DPJ · Transcription regulator, tetr family: “The crystal structure of a tetr transcription regulator from silicibacter pomeroyi dss”. X-ray diffraction, 17 pockets (best druggability 0.74). MolNFT v1 #61571 on GenesisL1: 3D structure…

PDB: 3DPJ
Type: protein
Length: 1,530 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transcription regulator, tetr family
UniProt: Q5LS67
Pockets: 17 · best druggability 0.74

Structure

x-ray diffraction · 4 distinct chains · 77% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Transcription regulator, tetr family	protein	194	79% helix, 1% strand	Q5LS67
B, D	Transcription regulator, tetr family	protein	190	74% helix, 0% strand	Q5LS67
E, G	Transcription regulator, tetr family	protein	193	79% helix, 0% strand	Q5LS67
F, H	Transcription regulator, tetr family	protein	188	76% helix, 0% strand	Q5LS67

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 30 copies · chains A, F, B, C, H, D, G, E
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 8 copies · chains A, B, C, D, E, F, G, H

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	135	0.74	0.93	33	EDO
2	864	0.73	0.78	73	EDO
3	280	0.73	0.86	24	MES
4	826	0.73	0.78	71	EDO
5	267	0.71	0.85	26	MES, EDO

Interfaces

14 interfaces between chains.

E–F · 1627 Å² buried · 23 hydrogen bonds · protein-protein
G–H · 1617 Å² buried · 18 hydrogen bonds · protein-protein
C–D · 1558 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1555 Å² buried · 16 hydrogen bonds · protein-protein
D–G · 385 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 52 modified (engineered).

Compared structures

3DPJ · The crystal structure of a TetR transcription regulator from Silicibacter pomeroyi DSS · the same entry in another collection · chain A against A, TM-score 1.00

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 Q5LS67
Elsewhere: RCSB PDB 3DPJ · PDBe 3DPJ · UniProt Q5LS67

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