2X15 | pdb_00002x15

The catalytically active fully closed conformation of human phosphoglycerate kinase in complex with ADP and 1,3- bisphosphoglycerate

PDB DOI: https://doi.org/10.2210/pdb2X15/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2009-12-21 Released: 2011-02-09
Deposition Author(s): Bowler, M.W., Cliff, M.J., Marston, J.P.M., Baxter, N.J., Hounslow, A.M.H., Varga, A.V., Szabo, J., Vas, M., Blackburn, G.M., Waltho, J.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.238 (Depositor), 0.240 (DCC)
R-Value Work:
0.192 (Depositor), 0.200 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

The Structure of Human Phosphoglycerate Kinase in its Fully Active Conformation in Complex with Ground State Analoges

Bowler, M.W., Cliff, M.J., Marston, J.P.M., Baxter, N.J., Hounslow, A.M.H., Varga, A.V., Szabo, J., Vas, M., Blackburn, G.M., Waltho, J.P.

To be published.

Macromolecule Content

Total Structure Weight: 45.95 kDa
Atom Count: 3,228
Modeled Residue Count: 408
Deposited Residue Count: 416
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHOGLYCERATE KINASE 1	A	416	Homo sapiens	Mutation(s): 0 EC: 2.7.2.3 (PDB Primary Data), 2.7.11.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00558 (Homo sapiens) Explore P00558 Go to UniProtKB: P00558
PHAROS: P00558 GTEx: ENSG00000102144
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00558
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
X15 Query on X15 Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	1,3-BISPHOSPHOGLYCERIC ACID C₃ H₈ O₁₀ P₂ LJQLQCAXBUHEAZ-UWTATZPHSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
3PG Query on 3PG Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	3-PHOSPHOGLYCERIC ACID C₃ H₇ O₇ P OSJPPGNTCRNQQC-UWTATZPHSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
3PG	BindingDB: 2X15	Kd: 1.09e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.238 (Depositor), 0.240 (DCC)
R-Value Work: 0.192 (Depositor), 0.200 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.73	α = 90
b = 91.75	β = 90
c = 108.31	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-02-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-02-09
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description

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Help and Resources

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The catalytically active fully closed conformation of human phosphoglycerate kinase in complex with ADP and 1,3- bisphosphoglycerate

The Structure of Human Phosphoglycerate Kinase in its Fully Active Conformation in Complex with Ground State Analoges

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations