2JKV | pdb_00002jkv

Structure of human Phosphogluconate Dehydrogenase in complex with NADPH at 2.53A

PDB DOI: https://doi.org/10.2210/pdb2JKV/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2008-09-01 Released: 2009-09-01
Deposition Author(s): Pilka, E.S., Kavanagh, K.L., von Delft, F., Muniz, J.R.C., Murray, J., Picaud, S., Guo, K., Edwards, A., Arrowsmith, C.H., Weigelt, J., Bountra, C., Oppermann, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.53 Å
R-Value Free:
0.207 (Depositor), 0.203 (DCC)
R-Value Work:
0.156 (Depositor), 0.155 (DCC)
R-Value Observed:
0.157 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Structure of Human Phosphogluconate Dehydrogenase in Complex with Nadph at 2.53A

Ng, S.S., von Delft, F., Pilka, E.S., Kavanagh, K.L., McDonough, M.A., Savitsky, P., Arrowsmith, C.H., Weigelt, J., Edwards, A., Sundstrom, M., Schofield, C.J., Oppermann, U.

To be published.

Macromolecule Content

Total Structure Weight: 339.84 kDa
Atom Count: 23,837
Modeled Residue Count: 2,881
Deposited Residue Count: 3,030
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING	A, B, C, D, E A, B, C, D, E, F	505	Homo sapiens	Mutation(s): 0 EC: 1.1.1.44
UniProt & NIH Common Fund Data Resources
Find proteins for P52209 (Homo sapiens) Explore P52209 Go to UniProtKB: P52209
PHAROS: P52209 GTEx: ENSG00000142657
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P52209
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain M [auth B] SDF format, chain S [auth C] SDF format, chain V [auth D] SDF format, chain Z [auth E] MOL2 format, chain G [auth A] MOL2 format, chain M [auth B] MOL2 format, chain S [auth C] MOL2 format, chain V [auth D] MOL2 format, chain Z [auth E] mmCIF format, chain G [auth A] mmCIF format, chain M [auth B] mmCIF format, chain S [auth C] mmCIF format, chain V [auth D] mmCIF format, chain Z [auth E]	G [auth A], M [auth B], S [auth C], V [auth D], Z [auth E]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain G [auth A] Focus chain M [auth B] Focus chain S [auth C] Focus chain V [auth D] Focus chain Z [auth E] Interactions & Density Focus chain G [auth A] Focus chain M [auth B] Focus chain S [auth C] Focus chain V [auth D] Focus chain Z [auth E]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain BA [auth E] SDF format, chain FA [auth F] SDF format, chain GA [auth F] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] MOL2 format, chain AA [auth E] MOL2 format, chain BA [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain GA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] mmCIF format, chain AA [auth E] mmCIF format, chain BA [auth E] mmCIF format, chain FA [auth F] mmCIF format, chain GA [auth F] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D]	AA [auth E] BA [auth E] FA [auth F] GA [auth F] I [auth A] AA [auth E], BA [auth E], FA [auth F], GA [auth F], I [auth A], J [auth A], P [auth B], Q [auth B], T [auth C], U [auth C], W [auth D], X [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth E] Focus chain BA [auth E] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain I [auth A] Focus chain J [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth E] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain I [auth A] Focus chain J [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain W [auth D] Focus chain X [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain DA [auth E] SDF format, chain EA [auth F] SDF format, chain H [auth A] SDF format, chain HA [auth F] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain Y [auth D] SDF format, chain R [auth B] SDF format, chain CA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain EA [auth F] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth F] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain Y [auth D] MOL2 format, chain R [auth B] MOL2 format, chain CA [auth E] mmCIF format, chain DA [auth E] mmCIF format, chain EA [auth F] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth F] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain Y [auth D] mmCIF format, chain R [auth B] mmCIF format, chain CA [auth E]	CA [auth E] DA [auth E] EA [auth F] H [auth A] HA [auth F] CA [auth E], DA [auth E], EA [auth F], H [auth A], HA [auth F], K [auth A], L [auth A], N [auth B], O [auth B], R [auth B], Y [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EA [auth F] Focus chain H [auth A] Focus chain HA [auth F] Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth B] Focus chain Y [auth D] Interactions & Density Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EA [auth F] Focus chain H [auth A] Focus chain HA [auth F] Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth B] Focus chain Y [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.53 Å
R-Value Free: 0.207 (Depositor), 0.203 (DCC)
R-Value Work: 0.156 (Depositor), 0.155 (DCC)
R-Value Observed: 0.157 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.643	α = 90
b = 204.714	β = 90.65
c = 170.319	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-09-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-09-01
Type: Initial release
Version 1.1: 2015-01-14
Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
Version 1.2: 2018-01-24
Changes: Database references
Version 1.3: 2018-02-21
Changes: Database references
Version 1.4: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description