2EIY | pdb_00002eiy

Crystal Structure of T.th.HB8 Branched-Chain Amino Acid Aminotransferase Complexed with 4-Methylvaleric Acid

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 
    0.201 (Depositor), 0.202 (DCC) 
  • R-Value Work: 
    0.189 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 
    0.189 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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

Literature

Crystal Structure of T.th.HB8 Branched-Chain Amino Acid Aminotransferase Complexed with 4-Methylvaleric Acid

Goto, M.

To be published.

Macromolecule Content 

  • Total Structure Weight: 103.9 kDa 
  • Atom Count: 7,991 
  • Modeled Residue Count: 895 
  • Deposited Residue Count: 924 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Branched-chain amino acid aminotransferase
A, B, C
308Thermus thermophilus HB8Mutation(s): 0 
EC: 2.6.1.42
UniProt
Find proteins for Q5SM19 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SM19 
Go to UniProtKB:  Q5SM19
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SM19
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PLP

Query on PLP


Download:Ideal Coordinates CCD File
D [auth A],
H [auth B],
L [auth C]		PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
MPD

Query on MPD


Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
J [auth B],
K [auth B],
N [auth C]		(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
4MV

Query on 4MV


Download:Ideal Coordinates CCD File
E [auth A],
I [auth B],
M [auth C]		4-METHYL VALERIC ACID
C6 H12 O2
FGKJLKRYENPLQH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free:  0.201 (Depositor), 0.202 (DCC) 
  • R-Value Work:  0.189 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.652α = 90
b = 143.652β = 90
c = 116.54γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MAR345data collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Released Date: 2008-03-18 
    • Deposition Author(s): Goto, M.

Revision History  (Full details and data files)

  • Version 1.0: 2008-03-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.2: 2017-10-11
    Changes: Refinement description
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description