4CVM | pdb_00004cvm

PaMurF in complex with AMP-PNP and UDP-MurNAc-tripeptide (mDAP)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 
    0.224 (Depositor), 0.233 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 

Literature

Pamurf in Complex with AMP-Pnp and Udp-Murnac-Tripeptide

Majce, V., Ruane, K.

To be published.

Macromolecule Content 

  • Total Structure Weight: 50.85 kDa 
  • Atom Count: 3,305 
  • Modeled Residue Count: 443 
  • Deposited Residue Count: 475 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
UDP-N-ACETYLMURAMOYL-TRIPEPTIDE--D-ALANYL-D- ALANINE LIGASE475Pseudomonas aeruginosa PAO1Mutation(s): 0 
EC: 6.3.2.10
UniProt
Find proteins for Q9HVZ7 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9HVZ7 
Go to UniProtKB:  Q9HVZ7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HVZ7
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP

Query on ANP


Download:Ideal Coordinates CCD File
F [auth A]PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
UDP

Query on UDP


Download:Ideal Coordinates CCD File
C [auth A]URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
MUB

Query on MUB


Download:Ideal Coordinates CCD File
D [auth A]N-acetyl-alpha-muramic acid
C11 H19 N O8
MNLRQHMNZILYPY-MDMHTWEWSA-N
FGA

Query on FGA


Download:Ideal Coordinates CCD File
E [auth A]GAMMA-D-GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-GSVOUGTGSA-N
ALA

Query on ALA


Download:Ideal Coordinates CCD File
B [auth A]ALANINE
C3 H7 N O2
QNAYBMKLOCPYGJ-REOHCLBHSA-N
MG

Query on MG


Download:Ideal Coordinates CCD File
G [auth A],
H [auth A]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free:  0.224 (Depositor), 0.233 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.54α = 90
b = 86.05β = 90
c = 88.24γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-22
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references, Structure summary