5OFM | pdb_00005ofm

Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with 5-amino-1-methyl-1H-indole

PDB DOI: https://doi.org/10.2210/pdb5OFM/pdb

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

Deposited: 2017-07-11 Released: 2017-08-16
Deposition Author(s): Unterlass, J.E., Basle, A., Blackburn, T.J., Tucker, J., Cano, C., Noble, M.E.M., Curtin, N.J.
Funding Organization(s): Cancer Research UK

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.249 (Depositor), 0.260 (DCC)
R-Value Work:
0.191 (Depositor), 0.200 (DCC)
R-Value Observed:
0.194 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5OFM

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

Literature

Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with 5-amino-1-methyl-1H-indole

Unterlass, J.E., Curtin, N.J.

To be published.

Macromolecule Content

Total Structure Weight: 48.16 kDa
Atom Count: 3,416
Modeled Residue Count: 390
Deposited Residue Count: 446
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-3-phosphoglycerate dehydrogenase	A [auth B], B [auth A]	223	Homo sapiens	Mutation(s): 0 Gene Names: PHGDH, PGDH3 EC: 1.1.1.95 (PDB Primary Data), 1.1.1.399 (PDB Primary Data), 1.1.1.37 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O43175 (Homo sapiens) Explore O43175 Go to UniProtKB: O43175
PHAROS: O43175 GTEx: ENSG00000092621
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O43175
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9TT Query on 9TT Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth B]	C [auth B], D [auth A]	1-methylindol-5-amine C₉ H₁₀ N₂ PGTSGPCXPIFQEL-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain D [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
9TT	BindingDB: 5OFM	Kd: 1.11e+7 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.249 (Depositor), 0.260 (DCC)
R-Value Work: 0.191 (Depositor), 0.200 (DCC)
R-Value Observed: 0.194 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.342	α = 97.91
b = 45.86	β = 110.74
c = 56.175	γ = 106.39

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-08-16

Deposition Author(s):

Unterlass, J.E.

Blackburn, T.J.

Funding Organization	Location	Grant Number
Cancer Research UK	United Kingdom	C2115/A21421

Revision History (Full details and data files)

Version 1.0: 2017-08-16
Type: Initial release
Version 1.1: 2018-04-18
Changes: Data collection, Database references
Version 1.2: 2024-05-08
Changes: Data collection, Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.