6I34

Crystal structure of Neanderthal glycine decarboxylase (P-protein)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural insights in human glycine decarboxylase and comparison with the Neanderthal variant

Van Laer, B.Kapp, U.Signor, L.Leonard, G.Mueller-Dieckmann, C.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Neanderthal Glycine decarboxylase
A, B, C, D
984Homo sapiens neanderthalensisMutation(s): 0 
EC: 1.4.4.2
UniProt & NIH Common Fund Data Resources
Find proteins for P23378 (Homo sapiens)
Explore P23378 
Go to UniProtKB:  P23378
PHAROS:  P23378
GTEx:  ENSG00000178445 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23378
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PLP
Query on PLP

Download Ideal Coordinates CCD File 
E [auth A],
L [auth B],
Q [auth C],
Z [auth D]
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
I [auth A],
P [auth B],
U [auth C],
V [auth C],
Y [auth D]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
CA [auth D],
J [auth A],
K [auth A],
W [auth C],
X [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
F [auth A]
G [auth A]
H [auth A]
AA [auth D],
BA [auth D],
F [auth A],
G [auth A],
H [auth A],
M [auth B],
N [auth B],
O [auth B],
R [auth C],
S [auth C],
T [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.873α = 90
b = 124.381β = 98.57
c = 201.304γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-20
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description