6ADE

Crystal structure of phosphorylated mutant of glyceraldehyde 3-phosphate dehydrogenase from human placenta at 3.15A resolution

PDB DOI: https://doi.org/10.2210/pdb6ADE/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2018-07-31 Released: 2018-08-22
Deposition Author(s): Dilawari, R., Singh, P.K., Raje, M., Sharma, S., Singh, T.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.15 Å
R-Value Free: 0.239
R-Value Work: 0.194
R-Value Observed: 0.196

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of phosphorylated mutant of glyceraldehyde 3-phosphate dehydrogenase from human placenta at 3.15A resolution

Dilawari, R., Singh, P.K., Raje, M., Sharma, S., Singh, T.P.

To be published.

Macromolecule Content

Total Structure Weight: 109.39 kDa
Atom Count: 7,679
Modelled Residue Count: 999
Deposited Residue Count: 1,005
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase	A, B, C	335	Homo sapiens	Mutation(s): 1 Gene Names: GAPDH, GAPD, CDABP0047, OK/SW-cl.12 EC: 1.2.1.12 (PDB Primary Data), 2.6.99 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P04406 (Homo sapiens) Explore P04406 Go to UniProtKB: P04406
PHAROS: P04406 GTEx: ENSG00000111640
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04406
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP Query on SEP	A, B, C	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.15 Å
R-Value Free: 0.239
R-Value Work: 0.194
R-Value Observed: 0.196
Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.78	α = 90
b = 131.68	β = 90
c = 220.64	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-08-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-08-22
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.