7CVP

The Crystal Structure of human PHGDH from Biortus.

PDB DOI: https://doi.org/10.2210/pdb7CVP/pdb

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

Deposited: 2020-08-26 Released: 2020-09-09
Deposition Author(s): Wang, F., Lv, Z., Cheng, W., Lin, D., Miao, Q., Huang, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.320
R-Value Work: 0.261

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The Crystal Structure of human PHGDH from Biortus.

Wang, F., Lv, Z., Cheng, W., Lin, D., Miao, Q., Huang, Y.

To be published.

Macromolecule Content

Total Structure Weight: 72.18 kDa
Atom Count: 3,671
Modelled Residue Count: 496
Deposited Residue Count: 658
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-3-phosphoglycerate dehydrogenase	A, B	329	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

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 C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.320
R-Value Work: 0.261
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.101	α = 90
b = 121.638	β = 99.974
c = 59.372	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2020-09-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-09-09
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Database references, Derived calculations, Refinement description

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Deposit Data

Help and Resources

7CVP

The Crystal Structure of human PHGDH from Biortus.

The Crystal Structure of human PHGDH from Biortus.

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)