6BFG

Crystal structure of monotopic membrane protein (S)-mandelate dehydrogenase

  • Classification: OXIDOREDUCTASE
  • Organism(s): Pseudomonas putida
  • Expression System: Escherichia coli

  • Deposited: 2017-10-26 Released: 2018-08-15 
  • Deposition Author(s): Sukumar, N.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences; National Institutes of Health 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of the monotopic membrane protein (S)-mandelate dehydrogenase at 2.2 angstrom resolution.

Sukumar, N.Liu, S.Li, W.Mathews, F.S.Mitra, B.Kandavelu, P.

(2018) Biochimie 154: 45-54


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
(S)-mandelate dehydrogenase
A, B
399Pseudomonas putidaMutation(s): 0 
Gene Names: mdlB
EC: 1.1.99.31
Membrane protein
mpstruct
Group: 
MONOTOPIC MEMBRANE PROTEINS
Sub Group: 
Dehydrogenases
Protein: 
(S)-Mandelate dehydrogenase (MDH)
Find proteins for P20932 (Pseudomonas putida)
Go to UniProtKB:  P20932
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

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B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
NA
Query on NA

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B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CIT
Query on CIT

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A
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FMN
Query on FMN

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A, B
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
GOL
Query on GOL

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A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
LMT
Query on LMT

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B
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
PEG
Query on PEG

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B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.197 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 123.358α = 90.00
b = 129.879β = 90.00
c = 143.260γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling
PHENIXphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-10-26 
  • Released Date: 2018-08-15 
  • Deposition Author(s): Sukumar, N.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM103403
National Institutes of HealthUnited StatesS10OD021527

Revision History 

  • Version 1.0: 2018-08-15
    Type: Initial release
  • Version 1.1: 2018-11-07
    Type: Data collection, Database references