5OFM

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

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
Modelled Residue Count: 390
Deposited Residue Count: 446
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O43175
Sequence Annotations Expand
Reference Sequence LOADING

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 C [auth B] SDF format, chain D [auth A] MOL2 format, chain C [auth B] MOL2 format, chain D [auth A] mmCIF format, chain C [auth B] mmCIF format, chain D [auth A]	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] Interactions & Density 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

View Full Validation Report

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

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.