8HPC | pdb_00008hpc

Crystal structure of C171A Mutant of N-carbamyl-D-amino acid amidohydrolase complexed with N-carbamyl-D-Hydroxyphenylglycine

PDB DOI: https://doi.org/10.2210/pdb8HPC/pdb

Classification: HYDROLASE
Organism(s): Agrobacterium sp. KNK712
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2022-12-12 Released: 2023-12-20
Deposition Author(s): Zhang, L.D., Song, W.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.52 Å
R-Value Free:
0.253 (Depositor), 0.232 (DCC)
R-Value Work:
0.218 (Depositor), 0.202 (DCC)
R-Value Observed:
0.220 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Production of D-p-hydroxyphenylglycine by double-enzyme cascade

Zhang, L.D., Song, W.

To be published.

Macromolecule Content

Total Structure Weight: 276.07 kDa
Atom Count: 19,517
Modeled Residue Count: 2,403
Deposited Residue Count: 2,432
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-carbamoyl-D-amino acid hydrolase	A, B, C, D, E A, B, C, D, E, F, G, H	304	Agrobacterium sp. KNK712	Mutation(s): 1 EC: 3.5.1.77
UniProt
Find proteins for P60327 (Agrobacterium sp. (strain KNK712)) Explore P60327 Go to UniProtKB: P60327
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60327
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
M9L (Subject of Investigation/LOI) Query on M9L Download:Ideal Coordinates CCD File SDF format, chain P [auth H] SDF format, chain O [auth G] SDF format, chain N [auth F] SDF format, chain M [auth E] SDF format, chain L [auth D] SDF format, chain K [auth C] SDF format, chain J [auth B] SDF format, chain I [auth A] MOL2 format, chain P [auth H] MOL2 format, chain O [auth G] MOL2 format, chain N [auth F] MOL2 format, chain M [auth E] MOL2 format, chain L [auth D] MOL2 format, chain K [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth A] mmCIF format, chain P [auth H] mmCIF format, chain O [auth G] mmCIF format, chain N [auth F] mmCIF format, chain M [auth E] mmCIF format, chain L [auth D] mmCIF format, chain K [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth A]	I [auth A] J [auth B] K [auth C] L [auth D] M [auth E] I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	(2~{R})-2-(aminocarbonylamino)-2-(4-hydroxyphenyl)ethanoic acid C₉ H₁₀ N₂ O₄ GSHIDXLOTQDUAV-SSDOTTSWSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth G] Focus chain P [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth G] Focus chain P [auth H]