4BHG | pdb_00004bhg

Three dimensional structure of human gamma-butyrobetaine hydroxylase in complex with 3-(1-Ethyl-1,1-dimethylhydrazin-1-ium-2-yl)propanoate

PDB DOI: https://doi.org/10.2210/pdb4BHG/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Saccharomyces cerevisiae
Mutation(s): No

Deposited: 2013-04-02 Released: 2014-04-16
Deposition Author(s): Tars, K., Leitans, J., Kazaks, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.190 (Depositor), 0.199 (DCC)
R-Value Work:
0.151 (Depositor), 0.161 (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 1.4 of the entry. See complete history.

Literature

Three Dimensional Structure of Human Gamma-Butyrobetaine Hydroxylase in Complex with 3-(1-Ethyl-1,1-Dimethylhydrazin-1-Ium-2-Yl)Propanoate

Tars, K., Leitans, J., Kazaks, A.

To be published.

Macromolecule Content

Total Structure Weight: 45.46 kDa
Atom Count: 3,595
Modeled Residue Count: 384
Deposited Residue Count: 387
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GAMMA-BUTYROBETAINE DIOXYGENASE	A	387	Homo sapiens	Mutation(s): 0 EC: 1.14.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O75936 (Homo sapiens) Explore O75936 Go to UniProtKB: O75936
PHAROS: O75936 GTEx: ENSG00000129151
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O75936
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
C2T Query on C2T 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]	3-(1-Ethyl-1,1-dimethylhydrazin-1-ium-2-yl)propanoic acid C₇ H₁₇ N₂ O₂ VFMQJOHSAQMQEH-UHFFFAOYSA-O		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
OGA Query on OGA 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]	N-OXALYLGLYCINE C₄ H₅ N O₅ BIMZLRFONYSTPT-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
16D Query on 16D Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	HEXANE-1,6-DIAMINE C₆ H₁₆ N₂ NAQMVNRVTILPCV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], F [auth A], G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.190 (Depositor), 0.199 (DCC)
R-Value Work: 0.151 (Depositor), 0.161 (DCC)
R-Value Observed: 0.153 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.18	α = 90
b = 108.18	β = 90
c = 203.18	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-04-16

Deposition Author(s):

Tars, K.

Leitans, J.

Kazaks, A.

Revision History (Full details and data files)

Version 1.0: 2014-04-16
Type: Initial release
Version 1.1: 2018-01-17
Changes: Data collection
Version 1.2: 2019-01-30
Changes: Data collection, Experimental preparation
Version 1.3: 2019-02-06
Changes: Data collection, Experimental preparation
Version 1.4: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description