5FVN

X-ray crystal structure of Enterobacter cloacae OmpE36 porin

Structural Biology Knowledgebase: 5FVN SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.183
  • R-Value Work: 0.155

Literature

Macromolecules
Sequence Display for 5FVN

Classification: MEMBRANE PROTEIN

Total Structure Weight: 262434.41

Macromolecule Entities
Molecule Chains Length Organism Details
OMPC PORIN A, B, C..., D, E, FA, B, C, D, E, F 342 Enterobacter cloacae Fragment: RESIDUES 22-363
Gene Name(s): ompC AWS52_24050
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: mpstruc | Group: BETA-BARREL

Subgroup Name: Beta-Barrel Membrane Proteins: Porins and Relatives

Protein Name: OmpC homolog (OmpE36) with bound lipopolysaccharide (LPS)


Small Molecules
Ligands 11 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
C8E
Query on C8E

A, B, C, D, E, F (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
C16 H34 O5
FEOZZFHAVXYAMB-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Z9M
Query on Z9M

A, B, C, D, E, F 2-amino-2-deoxy-4-O-phosphono-beta-D-glucopyranose
C6 H14 N O8 P
QWDBGVNDGYUIAC-QZABAPFNSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
L1L
Query on L1L

A, B, C, D, E, F [(2R,3R,4R,5S,6R)-3-azanyl-6-(hydroxymethyl)- 4,5-bis(oxidanyl)oxan-2-yl] dihydrogen phosphate
C6 H14 N O8 P
YMJBYRVFGYXULK-QZABAPFNSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FTT
Query on FTT

A, B, C, D, E, F 3-HYDROXY-TETRADECANOIC ACID
3-HYDROXY-MYRISTIC ACID (Synonym)
C14 H28 O3
ATRNZOYKSNPPBF-CYBMUJFWSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
KDO
Query on KDO

A, B, C, D, E, F 3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID
C8 H14 O8
NNLZBVFSCVTSLA-HXUQBWEZSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MYR
Query on MYR

A, B, C, D, E, F MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GMH
Query on GMH

B, C, F L-GLYCERO-D-MANNO-HEPTOPYRANOSE
C7 H14 O7
BGWQRWREUZVRGI-QQABCQGCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DAO
Query on DAO

A, B, C, D, E, F LAURIC ACID
C12 H24 O2
POULHZVOKOAJMA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

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

A, B, C, D, E, F PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

C, F CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.183
  • R-Value Work: 0.155
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 109.75 α = 90.00
b = 123.26 β = 91.01
c = 116.01 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2016-02-09
  • Released Date: 2016-08-10
  • Deposition author(s): Arunmanee, W., Pathania, M., Soloyova, A., Brun, A., Ridley, H., Basle, A., vandenBerg, B., Lakey, J.H.

Revision History

  • 2016-09-28
    Type: Citation | Details: JRNL
  • 2016-08-17
    Type: Citation | Details: JRNL