5TSO | pdb_00005tso

CRYSTAL STRUCTURE OF GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM PIG MUSCLE COMPLEXED WITH ORTHOPHENANTHROLINE AT 1.90 ANGSTROM RESOLUTION

PDB DOI: https://doi.org/10.2210/pdb5TSO/pdb

Classification: OXIDOREDUCTASE
Organism(s): Sus scrofa
Mutation(s): No

Deposited: 2016-10-30 Released: 2017-05-03
Deposition Author(s): Dimova, M., Devedjiev, Y.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.200 (Depositor), 0.202 (DCC)
R-Value Work:
0.132 (Depositor), 0.135 (DCC)
R-Value Observed:
0.133 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Novel Enhancer Binding Site Found In Bacteria And Eukaryota But Not In Archea.

Dimova, M., Devedjiev, Y.D.

To be published.

Macromolecule Content

Total Structure Weight: 112.06 kDa
Atom Count: 8,698
Modeled Residue Count: 996
Deposited Residue Count: 999
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase	A [auth P], B [auth R], C [auth S]	333	Sus scrofa	Mutation(s): 0 EC: 1.2.1.12 (PDB Primary Data), 2.6.99 (PDB Primary Data)
UniProt
Find proteins for P00355 (Sus scrofa) Explore P00355 Go to UniProtKB: P00355
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00355
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain F [auth P] SDF format, chain O [auth R] SDF format, chain X [auth S] MOL2 format, chain F [auth P] MOL2 format, chain O [auth R] MOL2 format, chain X [auth S] mmCIF format, chain F [auth P] mmCIF format, chain O [auth R] mmCIF format, chain X [auth S]	F [auth P], O [auth R], X [auth S]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain F [auth P] Focus chain O [auth R] Focus chain X [auth S] Interactions & Density Focus chain F [auth P] Focus chain O [auth R] Focus chain X [auth S]
PHN Query on PHN Download:Ideal Coordinates CCD File SDF format, chain K [auth R] SDF format, chain L [auth R] SDF format, chain T [auth S] SDF format, chain U [auth S] MOL2 format, chain K [auth R] MOL2 format, chain L [auth R] MOL2 format, chain T [auth S] MOL2 format, chain U [auth S] mmCIF format, chain K [auth R] mmCIF format, chain L [auth R] mmCIF format, chain T [auth S] mmCIF format, chain U [auth S]	K [auth R], L [auth R], T [auth S], U [auth S]	1,10-PHENANTHROLINE C₁₂ H₈ N₂ DGEZNRSVGBDHLK-UHFFFAOYSA-N		Interactions Focus chain K [auth R] Focus chain L [auth R] Focus chain T [auth S] Focus chain U [auth S] Interactions & Density Focus chain K [auth R] Focus chain L [auth R] Focus chain T [auth S] Focus chain U [auth S]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth P] SDF format, chain E [auth P] SDF format, chain G [auth P] SDF format, chain H [auth P] SDF format, chain I [auth P] SDF format, chain M [auth R] SDF format, chain N [auth R] SDF format, chain P [auth R] SDF format, chain Q [auth R] SDF format, chain V [auth S] SDF format, chain W [auth S] MOL2 format, chain D [auth P] MOL2 format, chain E [auth P] MOL2 format, chain G [auth P] MOL2 format, chain H [auth P] MOL2 format, chain I [auth P] MOL2 format, chain M [auth R] MOL2 format, chain N [auth R] MOL2 format, chain P [auth R] MOL2 format, chain Q [auth R] MOL2 format, chain V [auth S] MOL2 format, chain W [auth S] mmCIF format, chain D [auth P] mmCIF format, chain E [auth P] mmCIF format, chain G [auth P] mmCIF format, chain H [auth P] mmCIF format, chain I [auth P] mmCIF format, chain M [auth R] mmCIF format, chain N [auth R] mmCIF format, chain P [auth R] mmCIF format, chain Q [auth R] mmCIF format, chain V [auth S] mmCIF format, chain W [auth S]	D [auth P] E [auth P] G [auth P] H [auth P] I [auth P] D [auth P], E [auth P], G [auth P], H [auth P], I [auth P], M [auth R], N [auth R], P [auth R], Q [auth R], V [auth S], W [auth S]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth P] Focus chain E [auth P] Focus chain G [auth P] Focus chain H [auth P] Focus chain I [auth P] Focus chain M [auth R] Focus chain N [auth R] Focus chain P [auth R] Focus chain Q [auth R] Focus chain V [auth S] Focus chain W [auth S] Interactions & Density Focus chain D [auth P] Focus chain E [auth P] Focus chain G [auth P] Focus chain H [auth P] Focus chain I [auth P] Focus chain M [auth R] Focus chain N [auth R] Focus chain P [auth R] Focus chain Q [auth R] Focus chain V [auth S] Focus chain W [auth S]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain AA [auth S] SDF format, chain BA [auth S] SDF format, chain J [auth P] SDF format, chain R SDF format, chain S [auth R] SDF format, chain Y [auth S] SDF format, chain Z [auth S] MOL2 format, chain AA [auth S] MOL2 format, chain BA [auth S] MOL2 format, chain J [auth P] MOL2 format, chain R MOL2 format, chain S [auth R] MOL2 format, chain Y [auth S] MOL2 format, chain Z [auth S] mmCIF format, chain AA [auth S] mmCIF format, chain BA [auth S] mmCIF format, chain J [auth P] mmCIF format, chain R mmCIF format, chain S [auth R] mmCIF format, chain Y [auth S] mmCIF format, chain Z [auth S]	AA [auth S] BA [auth S] J [auth P] R S [auth R] AA [auth S], BA [auth S], J [auth P], R, S [auth R], Y [auth S], Z [auth S]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth S] Focus chain BA [auth S] Focus chain J [auth P] Focus chain R Focus chain S [auth R] Focus chain Y [auth S] Focus chain Z [auth S] Interactions & Density Focus chain AA [auth S] Focus chain BA [auth S] Focus chain J [auth P] Focus chain R Focus chain S [auth R] Focus chain Y [auth S] Focus chain Z [auth S]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.200 (Depositor), 0.202 (DCC)
R-Value Work: 0.132 (Depositor), 0.135 (DCC)
R-Value Observed: 0.133 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.48	α = 90
b = 133.52	β = 90
c = 210.32	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
AMoRE	phasing
DENZO	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2017-05-03

Deposition Author(s):

Dimova, M.

Devedjiev, Y.D.

Revision History (Full details and data files)

Version 1.0: 2017-05-03
Type: Initial release
Version 1.1: 2017-05-31
Changes: Atomic model
Version 1.2: 2018-01-31
Changes: Database references
Version 1.3: 2023-10-04
Changes: Data collection, Database references, Refinement description