5ZS7

Acetylation of lysine 100 in Phosphoglycerate mutase 1

  • Classification: ISOMERASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2018-04-28 Released: 2019-05-22 
  • Deposition Author(s): Jiang, L.L., Zhou, L.
  • Funding Organization(s): National Natural Science Foundation of China, Shanghai Municipal committee of Science and Technology, The program for Shanghai Rising Star

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Acetylation of lysine 100 in Phosphoglycerate mutase 1

Jiang, L.L., Zhou, L.

To be published.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphoglycerate mutase 1A [auth B]233Homo sapiensMutation(s): 0 
Gene Names: PGAM1, PGAMA, CDABP0006
EC: 5.4.2.11 (PDB Primary Data), 5.4.2.4 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P18669 (Homo sapiens)
Explore P18669 
Go to UniProtKB:  P18669
PHAROS:  P18669
GTEx:  ENSG00000171314 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18669
Sequence Annotations
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphoglycerate mutase 1B [auth C]234Homo sapiensMutation(s): 0 
Gene Names: PGAM1, PGAMA, CDABP0006
EC: 5.4.2.11 (PDB Primary Data), 5.4.2.4 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P18669 (Homo sapiens)
Explore P18669 
Go to UniProtKB:  P18669
PHAROS:  P18669
GTEx:  ENSG00000171314 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18669
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MES
Query on MES
Download Ideal Coordinates CCD File 
C
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
CL
Query on CL
Download Ideal Coordinates CCD File 
D [auth C]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
ALY
Query on ALY		B [auth C]L-PEPTIDE LINKINGC8 H16 N2 O3LYS
NEP
Query on NEP		B [auth C]L-PEPTIDE LINKINGC6 H10 N3 O5 PHIS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.833α = 90
b = 82.827β = 90
c = 100.232γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
PHASERphasing

Structure Validation

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View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina21472026
National Natural Science Foundation of ChinaChina31571479
National Natural Science Foundation of ChinaChina81622038
National Natural Science Foundation of ChinaChina81772965
Shanghai Municipal committee of Science and TechnologyChina14XD1400300
The program for Shanghai Rising StarChina15QA1400300

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-22
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description