7EBY

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

PDB DOI: https://doi.org/10.2210/pdb7EBY/pdb

Classification: HYDROLASE
Organism(s): Cupriavidus sp. P4-10-C
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-03-11 Released: 2022-01-26
Deposition Author(s): Yamasaki, M., Sumida, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.252
R-Value Work: 0.204
R-Value Observed: 0.206

wwPDB Validation 3D Report Full Report

This is version 1.1 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: 548.18 kDa
Atom Count: 38,729
Modelled Residue Count: 4,569
Deposited Residue Count: 4,944
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-succinylase	A, B, C, D, E A, B, C, D, E, F	824	Cupriavidus sp. P4-10-C	Mutation(s): 0 Gene Names: DSA
UniProt
Find proteins for A0A0N7KZ58 (Cupriavidus sp. P4-10-C) Explore A0A0N7KZ58 Go to UniProtKB: A0A0N7KZ58
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0N7KZ58
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain KA [auth E] SDF format, chain LA [auth E] SDF format, chain O [auth B] SDF format, chain QA [auth F] SDF format, chain RA [auth F] SDF format, chain SA [auth F] SDF format, chain T [auth C] SDF format, chain TA [auth F] SDF format, chain U [auth C] SDF format, chain UA [auth F] SDF format, chain V [auth C] SDF format, chain W [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain KA [auth E] MOL2 format, chain LA [auth E] MOL2 format, chain O [auth B] MOL2 format, chain QA [auth F] MOL2 format, chain RA [auth F] MOL2 format, chain SA [auth F] MOL2 format, chain T [auth C] MOL2 format, chain TA [auth F] MOL2 format, chain U [auth C] MOL2 format, chain UA [auth F] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C]	BA [auth D] CA [auth D] DA [auth D] EA [auth D] FA [auth D] BA [auth D], CA [auth D], DA [auth D], EA [auth D], FA [auth D], G [auth A], H [auth A], I [auth A], J [auth A], KA [auth E], LA [auth E], O [auth B], QA [auth F], RA [auth F], SA [auth F], T [auth C], TA [auth F], U [auth C], UA [auth F], V [auth C], W [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain KA [auth E] Focus chain LA [auth E] Focus chain O [auth B] Focus chain QA [auth F] Focus chain RA [auth F] Focus chain SA [auth F] Focus chain T [auth C] Focus chain TA [auth F] Focus chain U [auth C] Focus chain UA [auth F] Focus chain V [auth C] Focus chain W [auth C] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain KA [auth E] Focus chain LA [auth E] Focus chain O [auth B] Focus chain QA [auth F] Focus chain RA [auth F] Focus chain SA [auth F] Focus chain T [auth C] Focus chain TA [auth F] Focus chain U [auth C] Focus chain UA [auth F] Focus chain V [auth C] Focus chain W [auth C]
CO3 Query on CO3 Download Ideal Coordinates CCD File SDF format, chain GA [auth D] SDF format, chain HA [auth D] SDF format, chain IA [auth D] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain MA [auth E] SDF format, chain NA [auth E] SDF format, chain OA [auth E] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain VA [auth F] SDF format, chain WA [auth F] SDF format, chain X [auth C] SDF format, chain XA [auth F] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain GA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain IA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth E] MOL2 format, chain NA [auth E] MOL2 format, chain OA [auth E] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain VA [auth F] MOL2 format, chain WA [auth F] MOL2 format, chain X [auth C] MOL2 format, chain XA [auth F] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C]	GA [auth D] HA [auth D] IA [auth D] K [auth A] L [auth A] GA [auth D], HA [auth D], IA [auth D], K [auth A], L [auth A], M [auth A], MA [auth E], NA [auth E], OA [auth E], P [auth B], Q [auth B], R [auth B], VA [auth F], WA [auth F], X [auth C], XA [auth F], Y [auth C], Z [auth C]	CARBONATE ION C O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-L		Interactions Focus chain GA [auth D] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain OA [auth E] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain VA [auth F] Focus chain WA [auth F] Focus chain X [auth C] Focus chain XA [auth F] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain GA [auth D] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain OA [auth E] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain VA [auth F] Focus chain WA [auth F] Focus chain X [auth C] Focus chain XA [auth F] Focus chain Y [auth C] Focus chain Z [auth C]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain JA [auth D] SDF format, chain N [auth A] SDF format, chain PA [auth E] SDF format, chain S [auth B] SDF format, chain YA [auth F] MOL2 format, chain AA [auth C] MOL2 format, chain JA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain PA [auth E] MOL2 format, chain S [auth B] MOL2 format, chain YA [auth F]	AA [auth C] JA [auth D] N [auth A] PA [auth E] S [auth B] AA [auth C], JA [auth D], N [auth A], PA [auth E], S [auth B], YA [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain JA [auth D] Focus chain N [auth A] Focus chain PA [auth E] Focus chain S [auth B] Focus chain YA [auth F] Interactions & Density Focus chain AA [auth C] Focus chain JA [auth D] Focus chain N [auth A] Focus chain PA [auth E] Focus chain S [auth B] Focus chain YA [auth F]