5B15

Crystal Structure of Metallo-beta-Lactamase SMB-1 Bound to Hydrolyzed Doripenem


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.138 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal Structure of Metallo-beta-Lactamase SMB-1 Bound to Hydrolyzed Doripenem

Wachino, J.Arakawa, Y.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Metallo-beta-lactamaseA262Serratia marcescensMutation(s): 0 
Gene Names: SMB-1
EC: 3.5.2.6
Find proteins for G5ELM3 (Serratia marcescens)
Explore G5ELM3 
Go to UniProtKB:  G5ELM3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DQM
Query on DQM

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A
(2~{S},3~{R},4~{S})-2-[(2~{S},3~{R})-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-3-methyl-4-[(3~{S},5~{S})-5-[(sulfamoylamino)methyl]pyrrolidin-3-yl]sulfanyl-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid
C15 H26 N4 O7 S2
FODJFDYENOTZNC-UNWFBNKDSA-N
 Ligand Interaction
SO4
Query on SO4

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

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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.138 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.01α = 107.57
b = 40.92β = 102.56
c = 45.32γ = 107.01
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-05-11
    Type: Initial release
  • Version 1.1: 2016-07-06
    Changes: Data collection