4YB4 | pdb_00004yb4

Crystal structure of homoisocitrate dehydrogenase from Thermus thermophilus in complex with homoisocitrate, magnesium ion (II) and NADH

PDB DOI: https://doi.org/10.2210/pdb4YB4/pdb

Classification: OXIDOREDUCTASE
Organism(s): Thermus thermophilus HB27
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-02-18 Released: 2016-03-09
Deposition Author(s): Takahashi, K., Tomita, T., Kuzuyama, T., Nishiyama, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.205 (Depositor), 0.210 (DCC)
R-Value Work:
0.150 (Depositor), 0.160 (DCC)
R-Value Observed:
0.153 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structure of homoisocitrate dehydrogenase from Thermus thermophilus in complex with homoisocitrate, magnesium(II) and NADH

Takahashi, K., Tomita, T., Kuzuyama, T., Nishiyama, M.

To be published.

Macromolecule Content

Total Structure Weight: 152.55 kDa
Atom Count: 11,169
Modeled Residue Count: 1,332
Deposited Residue Count: 1,336
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Homoisocitrate dehydrogenase	A, B, C, D	334	Thermus thermophilus HB27	Mutation(s): 0 Gene Names: hicd, hdh, hicdh, TT_C1012 EC: 1.1.1.87 (PDB Primary Data), 1.1.1.286 (UniProt)
UniProt
Find proteins for Q72IW9 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72IW9 Go to UniProtKB: Q72IW9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q72IW9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAI Query on NAI Download Ideal Coordinates CCD File SDF format, chain LA [auth C] SDF format, chain U [auth B] SDF format, chain GB [auth D] SDF format, chain G [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain U [auth B] MOL2 format, chain GB [auth D] MOL2 format, chain G [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain U [auth B] mmCIF format, chain GB [auth D] mmCIF format, chain G [auth A]	G [auth A], GB [auth D], LA [auth C], U [auth B]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C₂₁ H₂₉ N₇ O₁₄ P₂ BOPGDPNILDQYTO-NNYOXOHSSA-N		Interactions Focus chain G [auth A] Focus chain GB [auth D] Focus chain LA [auth C] Focus chain U [auth B] Interactions & Density Focus chain G [auth A] Focus chain GB [auth D] Focus chain LA [auth C] Focus chain U [auth B]
48Y Query on 48Y Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain T [auth B] SDF format, chain KA [auth C] SDF format, chain FB [auth D] MOL2 format, chain F [auth A] MOL2 format, chain T [auth B] MOL2 format, chain KA [auth C] MOL2 format, chain FB [auth D] mmCIF format, chain F [auth A] mmCIF format, chain T [auth B] mmCIF format, chain KA [auth C] mmCIF format, chain FB [auth D]	F [auth A], FB [auth D], KA [auth C], T [auth B]	(1R,2S)-1-hydroxybutane-1,2,4-tricarboxylic acid C₇ H₁₀ O₇ OEJZZCGRGVFWHK-WVZVXSGGSA-N		Interactions Focus chain F [auth A] Focus chain FB [auth D] Focus chain KA [auth C] Focus chain T [auth B] Interactions & Density Focus chain F [auth A] Focus chain FB [auth D] Focus chain KA [auth C] Focus chain T [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AB [auth C] SDF format, chain BA [auth B] SDF format, chain BB [auth C] SDF format, chain CB [auth C] SDF format, chain EA [auth B] SDF format, chain EB [auth C] SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain HA [auth B] SDF format, chain IA [auth B] SDF format, chain N [auth A] SDF format, chain NB [auth D] SDF format, chain OB [auth D] SDF format, chain PB [auth D] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain WA [auth C] SDF format, chain XA [auth C] SDF format, chain ZA [auth C] SDF format, chain YA [auth C] SDF format, chain VA [auth C] SDF format, chain RB [auth D] SDF format, chain QB [auth D] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain M [auth A] SDF format, chain DB [auth C] SDF format, chain DA [auth B] SDF format, chain CA [auth B] MOL2 format, chain AB [auth C] MOL2 format, chain BA [auth B] MOL2 format, chain BB [auth C] MOL2 format, chain CB [auth C] MOL2 format, chain EA [auth B] MOL2 format, chain EB [auth C] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain NB [auth D] MOL2 format, chain OB [auth D] MOL2 format, chain PB [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain WA [auth C] MOL2 format, chain XA [auth C] MOL2 format, chain ZA [auth C] MOL2 format, chain YA [auth C] MOL2 format, chain VA [auth C] MOL2 format, chain RB [auth D] MOL2 format, chain QB [auth D] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain M [auth A] MOL2 format, chain DB [auth C] MOL2 format, chain DA [auth B] MOL2 format, chain CA [auth B] mmCIF format, chain AB [auth C] mmCIF format, chain BA [auth B] mmCIF format, chain BB [auth C] mmCIF format, chain CB [auth C] mmCIF format, chain EA [auth B] mmCIF format, chain EB [auth C] mmCIF format, chain FA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain NB [auth D] mmCIF format, chain OB [auth D] mmCIF format, chain PB [auth D] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain WA [auth C] mmCIF format, chain XA [auth C] mmCIF format, chain ZA [auth C] mmCIF format, chain YA [auth C] mmCIF format, chain VA [auth C] mmCIF format, chain RB [auth D] mmCIF format, chain QB [auth D] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain M [auth A] mmCIF format, chain DB [auth C] mmCIF format, chain DA [auth B] mmCIF format, chain CA [auth B]	AB [auth C] BA [auth B] BB [auth C] CA [auth B] CB [auth C] AB [auth C], BA [auth B], BB [auth C], CA [auth B], CB [auth C], DA [auth B], DB [auth C], EA [auth B], EB [auth C], FA [auth B], GA [auth B], HA [auth B], IA [auth B], M [auth A], N [auth A], NB [auth D], O [auth A], OB [auth D], P [auth A], PB [auth D], Q [auth A], QB [auth D], R [auth A], RB [auth D], S [auth A], VA [auth C], WA [auth C], XA [auth C], YA [auth C], ZA [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AB [auth C] Focus chain BA [auth B] Focus chain BB [auth C] Focus chain CA [auth B] Focus chain CB [auth C] Focus chain DA [auth B] Focus chain DB [auth C] Focus chain EA [auth B] Focus chain EB [auth C] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain NB [auth D] Focus chain O [auth A] Focus chain OB [auth D] Focus chain P [auth A] Focus chain PB [auth D] Focus chain Q [auth A] Focus chain QB [auth D] Focus chain R [auth A] Focus chain RB [auth D] Focus chain S [auth A] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C] Interactions & Density Focus chain AB [auth C] Focus chain BA [auth B] Focus chain BB [auth C] Focus chain CA [auth B] Focus chain CB [auth C] Focus chain DA [auth B] Focus chain DB [auth C] Focus chain EA [auth B] Focus chain EB [auth C] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain NB [auth D] Focus chain O [auth A] Focus chain OB [auth D] Focus chain P [auth A] Focus chain PB [auth D] Focus chain Q [auth A] Focus chain QB [auth D] Focus chain R [auth A] Focus chain RB [auth D] Focus chain S [auth A] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain HB [auth D] SDF format, chain I [auth A] SDF format, chain IB [auth D] SDF format, chain JB [auth D] SDF format, chain K [auth A] SDF format, chain KB [auth D] SDF format, chain LB [auth D] SDF format, chain PA [auth C] SDF format, chain QA [auth C] SDF format, chain RA [auth C] SDF format, chain TA [auth C] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain UA [auth C] SDF format, chain SA [auth C] SDF format, chain OA [auth C] SDF format, chain NA [auth C] SDF format, chain MB [auth D] SDF format, chain L [auth A] SDF format, chain J [auth A] SDF format, chain AA [auth B] MOL2 format, chain HB [auth D] MOL2 format, chain I [auth A] MOL2 format, chain IB [auth D] MOL2 format, chain JB [auth D] MOL2 format, chain K [auth A] MOL2 format, chain KB [auth D] MOL2 format, chain LB [auth D] MOL2 format, chain PA [auth C] MOL2 format, chain QA [auth C] MOL2 format, chain RA [auth C] MOL2 format, chain TA [auth C] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain UA [auth C] MOL2 format, chain SA [auth C] MOL2 format, chain OA [auth C] MOL2 format, chain NA [auth C] MOL2 format, chain MB [auth D] MOL2 format, chain L [auth A] MOL2 format, chain J [auth A] MOL2 format, chain AA [auth B] mmCIF format, chain HB [auth D] mmCIF format, chain I [auth A] mmCIF format, chain IB [auth D] mmCIF format, chain JB [auth D] mmCIF format, chain K [auth A] mmCIF format, chain KB [auth D] mmCIF format, chain LB [auth D] mmCIF format, chain PA [auth C] mmCIF format, chain QA [auth C] mmCIF format, chain RA [auth C] mmCIF format, chain TA [auth C] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain UA [auth C] mmCIF format, chain SA [auth C] mmCIF format, chain OA [auth C] mmCIF format, chain NA [auth C] mmCIF format, chain MB [auth D] mmCIF format, chain L [auth A] mmCIF format, chain J [auth A] mmCIF format, chain AA [auth B]	AA [auth B] HB [auth D] I [auth A] IB [auth D] J [auth A] AA [auth B], HB [auth D], I [auth A], IB [auth D], J [auth A], JB [auth D], K [auth A], KB [auth D], L [auth A], LB [auth D], MB [auth D], NA [auth C], OA [auth C], PA [auth C], QA [auth C], RA [auth C], SA [auth C], TA [auth C], UA [auth C], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain HB [auth D] Focus chain I [auth A] Focus chain IB [auth D] Focus chain J [auth A] Focus chain JB [auth D] Focus chain K [auth A] Focus chain KB [auth D] Focus chain L [auth A] Focus chain LB [auth D] Focus chain MB [auth D] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain HB [auth D] Focus chain I [auth A] Focus chain IB [auth D] Focus chain J [auth A] Focus chain JB [auth D] Focus chain K [auth A] Focus chain KB [auth D] Focus chain L [auth A] Focus chain LB [auth D] Focus chain MB [auth D] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain MA [auth C] SDF format, chain JA [auth C] SDF format, chain H [auth A] MOL2 format, chain E [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain H [auth A] mmCIF format, chain E [auth A] mmCIF format, chain MA [auth C] mmCIF format, chain JA [auth C] mmCIF format, chain H [auth A]	E [auth A], H [auth A], JA [auth C], MA [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth A] Focus chain JA [auth C] Focus chain MA [auth C] Interactions & Density Focus chain E [auth A] Focus chain H [auth A] Focus chain JA [auth C] Focus chain MA [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.205 (Depositor), 0.210 (DCC)
R-Value Work: 0.150 (Depositor), 0.160 (DCC)
R-Value Observed: 0.153 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 159.663	α = 90
b = 159.663	β = 90
c = 148.517	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Coot	refinement
HKL-2000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-03-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-03-09
Type: Initial release
Version 1.1: 2020-02-05
Changes: Data collection, Derived calculations
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description