7O04: Shortened IpgC variant

Crystal structure of a shortened IpgC variant in complex with [(2-chloro-5-nitrophenyl)methyl](methyl)amine. Determined by X-ray diffraction at 1.74 Å resolution. Released 13 Apr 2022.

Method: X-ray diffraction
Resolution: 1.74 Å
Organism: Shigella flexneri
Chains: 2
Atoms: 2,424
Mol. weight: 33.25 kDa
Ligands: MG, 4AV
Released: 13 Apr 2022

Explore 7O04 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7O04 contains 17 α-helices and 0 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 9 helices, 0 β-strands

Element	Residues	Length
α-helix	12-21	10
α-helix	26-28	3
α-helix	33-48	16
α-helix	52-65	14
α-helix	70-82	13
α-helix	86-99	14
α-helix	105-116	12
α-helix	120-133	14
α-helix	137-149	13

Chain B: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	10-20	11
α-helix	33-48	16
α-helix	52-65	14
α-helix	70-82	13
α-helix	86-98	13
α-helix	105-116	12
α-helix	120-133	14
α-helix	137-149	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Chaperone protein IpgC	A, B	protein	143	Shigella flexneri	P0A2U4 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7O04_1 Chaperone protein IpgC (chains A, B)
GSISTAVIDAINSGATLKDINAIPDDMMDDIYSYAYDFYNKGRIEEAEVFFRFLCIYDFY
NVDYIMGLAAIYQIKEQFQQAADLYAVAFALGKNDYTPVFHTGQCQLRLKAPLKAKECFE
LVIQHSNDEKLKIKAQSYLDAIQ

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	3
4AV	1-(2-chloro-5-nitrophenyl)-N-methylmethanamine	C8 H9 Cl N2 O2	1

Water and common crystallization additives (CL, PEG) are not listed.

Primary citation

Crystal structure of a shortened IpgC variant in complex with [(2-chloro-5-nitrophenyl)methyl](methyl)amine. Gardonyi, M., Heine, A., Klebe, G. To be published.

Other PDB entries of the same protein (UniProt P0A2U4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7P42 1.5 Å, Crystal structure of IpgC in complex with a follow-up compound based on J2
7PE0 1.5 Å, Crystal structure of IpgC in complex with J52
7PEF 1.54 Å, Crystal structure of IpgC in complex with DMSO
7NRG 1.57 Å, Crystal structure of a shortened IpgC variant in complex with…
6SCB 1.58 Å, Crystal structure of a shortened IpgC variant with two bound Magnesium and two bound…
7O6S 1.58 Å, Crystal structure of a shortened IpgC variant in complex with…
7B1U 1.59 Å, Crystal structure of a shortened IpgC variant in complex with…
7NL8 1.59 Å, Crystal structure of a shortened IpgC variant in complex with 3-methylbenzohydrazide
7OWV 1.59 Å, Crystal structure of IpgC in complex with a follow-up compound based on J20
7AXY 1.63 Å, Crystal structure of a shortened IpgC variant in complex with…
7AZV 1.68 Å, Crystal structure of a shortened IpgC variant in complex with…
7AYW 1.78 Å, Crystal structure of a shortened IpgC variant in complex with 2H-isoindol-1-amine

Browse structure collections

About this viewer

MolViewer shows 7O04 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.