6IAQ | pdb_00006iaq

Structure of Amine Dehydrogenase from Mycobacterium smegmatis

PDB DOI: https://doi.org/10.2210/pdb6IAQ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Mycolicibacterium smegmatis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-11-27 Released: 2019-03-27
Deposition Author(s): Grogan, G., Vaxelaire-Vergne, C., Beloti, L., Mayol, O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free:
0.233 (Depositor), 0.238 (DCC)
R-Value Work:
0.200 (Depositor), 0.207 (DCC)
R-Value Observed:
0.202 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

A family of native amine dehydrogenases for the asymmetric reductive amination of ketones

Mayol, O., Bastard, K., Beloti, L., Frese, A., Turkenburg, J.P., Petit, J.-L., Mariage, A., Debard, A., Pellouin, V., Perret, A., de Berardinis, V., Zaparucha, A., Grogan, G., Vaxelaire-Vergne, C.

(2019) Nat Catal

DOI: https://doi.org/10.1038/s41929-019-0249-z

Macromolecule Content

Total Structure Weight: 149.17 kDa
Atom Count: 10,892
Modeled Residue Count: 1,348
Deposited Residue Count: 1,356
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrodipicolinate reductase N-terminus domain-containing protein	A, B, C, D	339	Mycolicibacterium smegmatis	Mutation(s): 0 Gene Names: dapB_2, ERS451418_03299 EC: 1.17.1.8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	F [auth A], H [auth B], J [auth C], L [auth D]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]