4QFP

Crystal structure of dipeptide binding protein from pseudoalteromonas sp. SM9913 in complex with Val-Thr


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.903 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural insights into the multispecific recognition of dipeptides of deep-sea gram-negative bacterium Pseudoalteromonas sp. strain SM9913

Li, C.Y.Chen, X.L.Qin, Q.L.Wang, P.Zhang, W.X.Xie, B.B.Su, H.N.Zhang, X.Y.Zhou, B.C.Zhang, Y.Z.

(2015) J. Bacteriol. 197: 1125-1134


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ABC transporter periplasmic peptide-binding protein
A, B
541Pseudoalteromonas sp. (strain SM9913)Mutation(s): 0 
Gene Names: dppA
Find proteins for A7Y7W1 (Pseudoalteromonas sp. (strain SM9913))
Go to UniProtKB:  A7Y7W1
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
VAL
Query on VAL

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Download CCD File 
A, B
VALINE
C5 H11 N O2
KZSNJWFQEVHDMF-BYPYZUCNSA-N
 Ligand Interaction
THR
Query on THR

Download SDF File 
Download CCD File 
A, B
THREONINE
C4 H9 N O3
AYFVYJQAPQTCCC-GBXIJSLDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.903 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.155 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 105.949α = 90.00
b = 105.949β = 90.00
c = 101.263γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
MLPHAREphasing
HKL-2000data collection
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-05-21 
  • Released Date: 2015-01-28 
  • Deposition Author(s): Li, C.Y., Zhang, Y.Z.

Revision History 

  • Version 1.0: 2015-01-28
    Type: Initial release
  • Version 1.1: 2018-10-17
    Type: Data collection, Database references