3RUM

New strategy to analyze structures of glycopeptide antibiotic-target complexes

Structural Biology Knowledgebase: 3RUM SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.219
  • R-Value Work: 0.176

Literature

Macromolecules
Sequence Display for 3RUM

Classification: SUGAR BINDING PROTEIN / ANTIBIOTIC

Total Structure Weight: 46510.10

Macromolecule Entities
Molecule Chains Length Organism Details
Maltose-binding periplasmic protein A 378 Escherichia coli Fragment: UNP RESIDUES 27-392
Gene Name(s): malE b4034 JW3994
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Ristocetin B, C 7 Amycolatopsis lurida

Membrane Protein

Source: inferred by homology | Group: ALPHA-HELICAL

Subgroup Name: ATP Binding Cassette (ABC) Transporters

Protein Name: MalFGK2-MBP Maltose uptake transporter complex


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

A MALTOSE
C12 H22 O11
GUBGYTABKSRVRQ-ASMJPISFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

B, C ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BGC
Query on BGC

B, C BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
RAM
Query on RAM

B, C ALPHA-L-RHAMNOSE
C6 H12 O5
SHZGCJCMOBCMKK-HGVZOGFYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BXY
Query on BXY

B, C alpha-D-arabinofuranose
C5 H10 O5
HMFHBZSHGGEWLO-MBMOQRBOSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
RST
Query on RST

B, C RISTOSAMINE
C6 H13 N O3
BBMKQGIZNKEDOX-KCDKBNATSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

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

A ISOPROPYL ALCOHOL
2-PROPANOL (Synonym)
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 7 Unique
ID Chains Type Formula 2D Diagram Parent
CCS
Query on CCS
A L-PEPTIDE LINKING C5 H9 N O4 S CYS
DAL
Query on DAL
A D-PEPTIDE LINKING C3 H7 N O2 --
GHP
Query on GHP
B, C D-PEPTIDE LINKING C8 H9 N O3 --
HTY
Query on HTY
B, C D-peptide linking C9 H11 N O4 --
MP4
Query on MP4
B, C L-peptide linking C9 H11 N O4 --
OMX
Query on OMX
B, C L-PEPTIDE LINKING C9 H11 N O4 TYR
MDF
Query on MDF
B, C L-PEPTIDE LINKING C9 H11 N O4 TYR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.219
  • R-Value Work: 0.176
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 57.83 α = 90.00
b = 75.00 β = 90.00
c = 90.78 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-05-05
  • Released Date: 2012-06-06
  • Deposition author(s): Economou, N.J., Weeks, S.D., Grasty, K.C., Nahoum, V., Loll, P.J.

Revision History

  • 2016-02-17
    Type: Linkage | Details: --
  • 2016-02-17
    Type: Non-polymer description | Details: --