4H2V

Crystal structure of Bradyrhizobium japonicum glycine:[carrier protein] ligase complexed with glycylated carrier protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.210
  • R-Value Work: 0.179

Literature

Macromolecules
Sequence Display for 4H2V

Classification: LIGASE

Total Structure Weight: 102707.30

Macromolecule Entities
Molecule Chains Length Organism Details
Amino acid--[acyl-carrier-protein] ligase 1 A, B 346 Bradyrhizobium diazoefficiens EC#: 6.2.1.n2 IUBMB
Gene Name(s): bll0957
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Aminoacyl carrier protein 1 C, D 110 Bradyrhizobium diazoefficiens Gene Name(s): bsr0959
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 8 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
H2V
Query on H2V

C S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]- beta-alanyl}amino)ethyl] aminoethanethioate
S-glycyl-4'-phosphopantetheine (Synonym)
C13 H26 N3 O8 P S
CGYKHWUDQZHKBD-LLVKDONJSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PNS
Query on PNS

D 4'-PHOSPHOPANTETHEINE
C11 H23 N2 O7 P S
JDMUPRLRUUMCTL-VIFPVBQESA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
AMP
Query on AMP

A, B ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

B PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

A ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.210
  • R-Value Work: 0.179
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 90.85 α = 90.00
b = 101.02 β = 90.00
c = 104.41 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-09-13
  • Released Date: 2013-03-06
  • Deposition author(s): Luic, M., Weygand-Durasevic, I., Ivic, N., Mocibob, M.

Revision History

  • Version 1_0: 2013-03-06

    Type: Initial release

  • Version 1_1: 2013-04-10

    Type: Database references

  • Version 1_2: 2013-05-29

    Type: Database references