4JQ9 | pdb_00004jq9

Dihydrolipoyl dehydrogenase of Escherichia coli pyruvate dehydrogenase complex

PDB DOI: https://doi.org/10.2210/pdb4JQ9/pdb

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

Deposited: 2013-03-20 Released: 2014-04-02
Deposition Author(s): Tietzel, M., Neumann, P., Meyer, D., Ficner, R., Tittmann, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.17 Å
R-Value Free:
0.208 (Depositor), 0.197 (DCC)
R-Value Work:
0.177 (Depositor)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Dihydrolipoyl dehydrogenase of Escherichia coli pyruvate dehydrogenase complex

Tietzel, M., Meyer, D., Schroeder-Tittmann, K., Neumann, P., Ficner, R., Tittmann, K.

To be published.

Macromolecule Content

Total Structure Weight: 313.62 kDa
Atom Count: 23,738
Modeled Residue Count: 2,820
Deposited Residue Count: 2,844
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrolipoyl dehydrogenase	A, B, C, D, E A, B, C, D, E, F	474	Escherichia coli	Mutation(s): 0 Gene Names: lpdA, lpd, BN17_45381, ECs0120, LF82_1218 EC: 1.8.1.4
UniProt
Find proteins for C3TQA2 (Escherichia coli) Explore C3TQA2 Go to UniProtKB: C3TQA2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C3TQA2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain GB [auth E] SDF format, chain HB [auth F] SDF format, chain LA [auth C] SDF format, chain R [auth A] SDF format, chain VA [auth D] SDF format, chain BA [auth B] MOL2 format, chain GB [auth E] MOL2 format, chain HB [auth F] MOL2 format, chain LA [auth C] MOL2 format, chain R [auth A] MOL2 format, chain VA [auth D] MOL2 format, chain BA [auth B] mmCIF format, chain GB [auth E] mmCIF format, chain HB [auth F] mmCIF format, chain LA [auth C] mmCIF format, chain R [auth A] mmCIF format, chain VA [auth D] mmCIF format, chain BA [auth B]	BA [auth B] GB [auth E] HB [auth F] LA [auth C] R [auth A] BA [auth B], GB [auth E], HB [auth F], LA [auth C], R [auth A], VA [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain BA [auth B] Focus chain GB [auth E] Focus chain HB [auth F] Focus chain LA [auth C] Focus chain R [auth A] Focus chain VA [auth D] Interactions & Density Focus chain BA [auth B] Focus chain GB [auth E] Focus chain HB [auth F] Focus chain LA [auth C] Focus chain R [auth A] Focus chain VA [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain FB [auth E] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain KA [auth C] SDF format, chain MA [auth D] SDF format, chain NA [auth D] SDF format, chain NB [auth F] SDF format, chain P [auth A] SDF format, chain PA [auth D] SDF format, chain QA [auth D] SDF format, chain S [auth B] SDF format, chain TA [auth D] SDF format, chain U [auth B] SDF format, chain UA [auth D] SDF format, chain V [auth B] SDF format, chain WA [auth E] SDF format, chain XA [auth E] SDF format, chain Y [auth B] SDF format, chain YA [auth E] SDF format, chain Z [auth B] SDF format, chain T [auth B] SDF format, chain Q [auth A] SDF format, chain OA [auth D] SDF format, chain IB [auth F] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain FB [auth E] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain MA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain NB [auth F] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain QA [auth D] MOL2 format, chain S [auth B] MOL2 format, chain TA [auth D] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth D] MOL2 format, chain V [auth B] MOL2 format, chain WA [auth E] MOL2 format, chain XA [auth E] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth E] MOL2 format, chain Z [auth B] MOL2 format, chain T [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain IB [auth F] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain FB [auth E] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain MA [auth D] mmCIF format, chain NA [auth D] mmCIF format, chain NB [auth F] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth D] mmCIF format, chain QA [auth D] mmCIF format, chain S [auth B] mmCIF format, chain TA [auth D] mmCIF format, chain U [auth B] mmCIF format, chain UA [auth D] mmCIF format, chain V [auth B] mmCIF format, chain WA [auth E] mmCIF format, chain XA [auth E] mmCIF format, chain Y [auth B] mmCIF format, chain YA [auth E] mmCIF format, chain Z [auth B] mmCIF format, chain T [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain OA [auth D] mmCIF format, chain IB [auth F] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	AA [auth B] CA [auth C] DA [auth C] FB [auth E] G [auth A] AA [auth B], CA [auth C], DA [auth C], FB [auth E], G [auth A], H [auth A], I [auth A], IB [auth F], J [auth A], KA [auth C], MA [auth D], NA [auth D], NB [auth F], OA [auth D], P [auth A], PA [auth D], Q [auth A], QA [auth D], S [auth B], T [auth B], TA [auth D], U [auth B], UA [auth D], V [auth B], WA [auth E], XA [auth E], Y [auth B], YA [auth E], Z [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth B] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain FB [auth E] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain IB [auth F] Focus chain J [auth A] Focus chain KA [auth C] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain NB [auth F] Focus chain OA [auth D] Focus chain P [auth A] Focus chain PA [auth D] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain S [auth B] Focus chain T [auth B] Focus chain TA [auth D] Focus chain U [auth B] Focus chain UA [auth D] Focus chain V [auth B] Focus chain WA [auth E] Focus chain XA [auth E] Focus chain Y [auth B] Focus chain YA [auth E] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain FB [auth E] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain IB [auth F] Focus chain J [auth A] Focus chain KA [auth C] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain NB [auth F] Focus chain OA [auth D] Focus chain P [auth A] Focus chain PA [auth D] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain S [auth B] Focus chain T [auth B] Focus chain TA [auth D] Focus chain U [auth B] Focus chain UA [auth D] Focus chain V [auth B] Focus chain WA [auth E] Focus chain XA [auth E] Focus chain Y [auth B] Focus chain YA [auth E] Focus chain Z [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain AB [auth E] SDF format, chain JB [auth F] SDF format, chain KB [auth F] SDF format, chain RA [auth D] SDF format, chain SA [auth D] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain ZA [auth E] SDF format, chain K [auth A] SDF format, chain EA [auth C] MOL2 format, chain AB [auth E] MOL2 format, chain JB [auth F] MOL2 format, chain KB [auth F] MOL2 format, chain RA [auth D] MOL2 format, chain SA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain ZA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain EA [auth C] mmCIF format, chain AB [auth E] mmCIF format, chain JB [auth F] mmCIF format, chain KB [auth F] mmCIF format, chain RA [auth D] mmCIF format, chain SA [auth D] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain ZA [auth E] mmCIF format, chain K [auth A] mmCIF format, chain EA [auth C]	AB [auth E] EA [auth C] JB [auth F] K [auth A] KB [auth F] AB [auth E], EA [auth C], JB [auth F], K [auth A], KB [auth F], RA [auth D], SA [auth D], W [auth B], X [auth B], ZA [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AB [auth E] Focus chain EA [auth C] Focus chain JB [auth F] Focus chain K [auth A] Focus chain KB [auth F] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain W [auth B] Focus chain X [auth B] Focus chain ZA [auth E] Interactions & Density Focus chain AB [auth E] Focus chain EA [auth C] Focus chain JB [auth F] Focus chain K [auth A] Focus chain KB [auth F] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain W [auth B] Focus chain X [auth B] Focus chain ZA [auth E]
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain BB [auth E] SDF format, chain FA [auth C] SDF format, chain L [auth A] SDF format, chain M [auth A] MOL2 format, chain BB [auth E] MOL2 format, chain FA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] mmCIF format, chain BB [auth E] mmCIF format, chain FA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A]	BB [auth E], FA [auth C], L [auth A], M [auth A]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain BB [auth E] Focus chain FA [auth C] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain BB [auth E] Focus chain FA [auth C] Focus chain L [auth A] Focus chain M [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain DB [auth E] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain JA [auth C] SDF format, chain LB [auth F] SDF format, chain MB [auth F] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain EB [auth E] SDF format, chain CB [auth E] MOL2 format, chain DB [auth E] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain LB [auth F] MOL2 format, chain MB [auth F] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain EB [auth E] MOL2 format, chain CB [auth E] mmCIF format, chain DB [auth E] mmCIF format, chain GA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain JA [auth C] mmCIF format, chain LB [auth F] mmCIF format, chain MB [auth F] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain EB [auth E] mmCIF format, chain CB [auth E]	CB [auth E] DB [auth E] EB [auth E] GA [auth C] HA [auth C] CB [auth E], DB [auth E], EB [auth E], GA [auth C], HA [auth C], IA [auth C], JA [auth C], LB [auth F], MB [auth F], N [auth A], O [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain CB [auth E] Focus chain DB [auth E] Focus chain EB [auth E] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain LB [auth F] Focus chain MB [auth F] Focus chain N [auth A] Focus chain O [auth A] Interactions & Density Focus chain CB [auth E] Focus chain DB [auth E] Focus chain EB [auth E] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain LB [auth F] Focus chain MB [auth F] Focus chain N [auth A] Focus chain O [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.17 Å
R-Value Free: 0.208 (Depositor), 0.197 (DCC)
R-Value Work: 0.177 (Depositor)
R-Value Observed: 0.179 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.68	α = 90
b = 129.32	β = 90
c = 258.34	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
MxCuBE	data collection
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-04-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-04-02
Type: Initial release
Version 1.1: 2019-09-04
Changes: Advisory, Data collection
Version 1.2: 2023-09-20
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-11-27
Changes: Structure summary