2EJ0 | pdb_00002ej0

Crystal Structure of T.th.HB8 Branched-Chain Amino Acid Aminotransferase with Pyridoxamine 5'-phosphate

PDB DOI: https://doi.org/10.2210/pdb2EJ0/pdb

Classification: TRANSFERASE
Organism(s): Thermus thermophilus HB8
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2007-03-14 Released: 2008-03-18
Deposition Author(s): Goto, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.194 (Depositor), 0.190 (DCC)
R-Value Work:
0.179 (Depositor), 0.170 (DCC)
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 1.2 of the entry. See complete history.

Literature

Crystal Structure of T.th.HB8 Branched-Chain Amino Acid Aminotransferase with Pyridoxamine 5'-phosphate

Goto, M.

To be published.

Macromolecule Content

Total Structure Weight: 206.87 kDa
Atom Count: 15,706
Modeled Residue Count: 1,794
Deposited Residue Count: 1,848
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Branched-chain amino acid aminotransferase	A, B, C, D, E A, B, C, D, E, F	308	Thermus thermophilus HB8	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5SM19
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PMP Query on PMP Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain N [auth D] SDF format, chain Q [auth E] SDF format, chain S [auth F] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain S [auth F] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D] mmCIF format, chain Q [auth E] mmCIF format, chain S [auth F]	G [auth A] J [auth B] L [auth C] N [auth D] Q [auth E] G [auth A], J [auth B], L [auth C], N [auth D], Q [auth E], S [auth F]	4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE C₈ H₁₃ N₂ O₅ P ZMJGSOSNSPKHNH-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain Q [auth E] Focus chain S [auth F] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain Q [auth E] Focus chain S [auth F]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain O [auth D] SDF format, chain P [auth D] SDF format, chain R [auth E] SDF format, chain T [auth F] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] MOL2 format, chain R [auth E] MOL2 format, chain T [auth F] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth C] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D] mmCIF format, chain R [auth E] mmCIF format, chain T [auth F]	H [auth A] I [auth A] K [auth B] M [auth C] O [auth D] H [auth A], I [auth A], K [auth B], M [auth C], O [auth D], P [auth D], R [auth E], T [auth F]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain R [auth E] Focus chain T [auth F] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain R [auth E] Focus chain T [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.194 (Depositor), 0.190 (DCC)
R-Value Work: 0.179 (Depositor), 0.170 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.88	α = 90
b = 143.69	β = 90
c = 146.58	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

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Crystal Structure of T.th.HB8 Branched-Chain Amino Acid Aminotransferase with Pyridoxamine 5'-phosphate

Crystal Structure of T.th.HB8 Branched-Chain Amino Acid Aminotransferase with Pyridoxamine 5'-phosphate

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)

2EJ0 | pdb_00002ej0