5XDF | pdb_00005xdf

Homoserine dehydrogenase from Thermus thermophilus HB8 complexed with HSE

PDB DOI: https://doi.org/10.2210/pdb5XDF/pdb

Classification: OXIDOREDUCTASE
Organism(s): Thermus thermophilus HB8
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-03-28 Released: 2017-04-26
Deposition Author(s): Akai, S., Miyahara, I.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.219 (Depositor), 0.226 (DCC)
R-Value Work:
0.185 (Depositor), 0.195 (DCC)
R-Value Observed:
0.186 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Crystallographic study of homoserine dehydrogenase from Thermus thermophilus HB8

Akai, S., Ikushiro, H., Sawai, D., Hayashi, H., Kamiya, N., Miyahara, I.

To be published.

Macromolecule Content

Total Structure Weight: 71.44 kDa
Atom Count: 5,346
Modeled Residue Count: 653
Deposited Residue Count: 664
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Homoserine dehydrogenase	A, B	332	Thermus thermophilus HB8	Mutation(s): 0 Gene Names: TTHA0489 EC: 1.1.1.3
UniProt
Find proteins for Q5SL04 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SL04 Go to UniProtKB: Q5SL04
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SL04
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HSE Query on HSE Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	L-HOMOSERINE C₄ H₉ N O₃ UKAUYVFTDYCKQA-VKHMYHEASA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	E [auth A], H [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.219 (Depositor), 0.226 (DCC)
R-Value Work: 0.185 (Depositor), 0.195 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.625	α = 90
b = 119.625	β = 90
c = 145.02	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2017-04-26

Deposition Author(s):

Akai, S.

Miyahara, I.

Revision History (Full details and data files)

Version 1.0: 2017-04-26
Type: Initial release
Version 1.1: 2020-02-26
Changes: Data collection
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Database references

5XDF | pdb_00005xdf

Homoserine dehydrogenase from Thermus thermophilus HB8 complexed with HSE

Literature

Crystallographic study of homoserine dehydrogenase from Thermus thermophilus HB8

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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