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Crystal structure of SIGD4 in complex with its negative regulator rsda

Analyse Crystal structure of SIGD4 in complex with its negative regulator rsda in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3VEP
Type: protein
Length: 466 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uncharacterized protein RV3413C/MT3522; Probable RNA polymerase sigma-D factor
UniProt: P65081, P66811
Ligands: SO4
Pockets: 4 · best druggability 0.71

Structure

x-ray diffraction · 6 distinct chains · 74% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
X	Uncharacterized protein RV3413C/MT3522	protein	46	74% helix, 0% strand	P65081
D	Probable RNA polymerase sigma-D factor	protein	68	76% helix, 0% strand	P66811
C, J	Uncharacterized protein RV3413C/MT3522	protein	47	68% helix, 0% strand	P65081
A, E	Probable RNA polymerase sigma-D factor	protein	70	77% helix, 0% strand	P66811
G	Uncharacterized protein RV3413C/MT3522	protein	47	70% helix, 0% strand	P65081
H	Probable RNA polymerase sigma-D factor	protein	71	76% helix, 0% strand	P66811

Ligands and binding sites

SO4 · Sulfate ion · ion · 13 copies · chains X, A, D, C, E, J, H

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

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	730	0.71	0.78	74	empty
2	633	0.67	0.76	56	empty
3	159	0.50	0.78	27	SO4
4	168	0.47	0.76	26	SO4

Interfaces

14 interfaces between chains.

J–H · 1126 Å² buried · 10 hydrogen bonds · protein-protein
C–A · 1117 Å² buried · 10 hydrogen bonds · protein-protein
G–E · 1107 Å² buried · 10 hydrogen bonds · protein-protein
X–D · 1065 Å² buried · 9 hydrogen bonds · protein-protein
X–A · 147 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 8 modified (engineered).

Compared structures

3VEP · Crystal structure of SigD4 in complex with its negative regulator RsdA · the same entry in another collection · chain X against X, 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 P65081
Every structure of UniProt P66811
Elsewhere: RCSB PDB 3VEP · PDBe 3VEP · UniProt P65081 · UniProt P66811

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