7EA4 | pdb_00007ea4

Crystal Structure of L182E D-Succinylase (DSA) from Cupriavidus sp. P4-10-C

PDB DOI: https://doi.org/10.2210/pdb7EA4/pdb

Classification: HYDROLASE
Organism(s): Cupriavidus sp. P4-10-C
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2021-03-06 Released: 2022-01-26
Deposition Author(s): Yamasaki, M., Sumida, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.208 (Depositor), 0.208 (DCC)
R-Value Work:
0.164 (Depositor), 0.165 (DCC)
R-Value Observed:
0.167 (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

Protein Engineering of d-Succinylase from Cupriavidus sp. for d-Amino Acid Synthesis and the Structural Implications.

Sumida, Y., Yamasaki, M., Nishiya, Y., Kumagai, S., Yamada, T., Azuma, M.

(2021) Adv Synth Catal 363: 4770-4778

DOI: https://doi.org/10.1002/adsc.202100587

Macromolecule Content

Total Structure Weight: 182.94 kDa
Atom Count: 12,947
Modeled Residue Count: 1,523
Deposited Residue Count: 1,648
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-succinylase	A, B	824	Cupriavidus sp. P4-10-C	Mutation(s): 1 Gene Names: DSA
UniProt
Find proteins for A0A0N7KZ58 (Cupriavidus sp. P4-10-C) Explore A0A0N7KZ58 Go to UniProtKB: A0A0N7KZ58
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0N7KZ58
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CAD Query on CAD Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain C [auth A] MOL2 format, chain F [auth A] MOL2 format, chain C [auth A] mmCIF format, chain F [auth A] mmCIF format, chain C [auth A]	C [auth A], F [auth A]	CACODYLIC ACID C₂ H₇ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth A] Interactions & Density Focus chain C [auth A] Focus chain F [auth A]
SIN (Subject of Investigation/LOI) Query on SIN Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A], L [auth B], M [auth B], N [auth B]	SUCCINIC ACID C₄ H₆ O₄ KDYFGRWQOYBRFD-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
CO3 Query on CO3 Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	CARBONATE ION C O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain J [auth A] MOL2 format, chain O [auth B] MOL2 format, chain J [auth A] mmCIF format, chain O [auth B] mmCIF format, chain J [auth A]	J [auth A], O [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain O [auth B] Interactions & Density Focus chain J [auth A] Focus chain O [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain K [auth A] MOL2 format, chain P [auth B] MOL2 format, chain K [auth A] mmCIF format, chain P [auth B] mmCIF format, chain K [auth A]	K [auth A], P [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth A] Focus chain P [auth B] Interactions & Density Focus chain K [auth A] Focus chain P [auth B]