4NT9 | pdb_00004nt9

Crystal structure of an L,D-carboxypeptidase DacB from Streptococcus pneumonia

PDB DOI: https://doi.org/10.2210/pdb4NT9/pdb

Classification: HYDROLASE
Organism(s): Streptococcus pneumoniae TIGR4
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-12-02 Released: 2014-11-12
Deposition Author(s): Yang, Y.H., Zhang, J., Jiang, Y.L., Zhou, C.Z., Chen, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.71 Å
R-Value Free:
0.212 (Depositor), 0.210 (DCC)
R-Value Work:
0.177 (Depositor), 0.180 (DCC)
R-Value Observed:
0.179 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of an L,D-carboxypeptidase DacB from Streptococcus pneumonia

Yang, Y.H., Zhang, J., Jiang, Y.L., Zhou, C.Z., Chen, Y.

To be published.

Macromolecule Content

Total Structure Weight: 74.13 kDa
Atom Count: 4,833
Modeled Residue Count: 552
Deposited Residue Count: 657
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	A [auth B], B [auth A], C	219	Streptococcus pneumoniae TIGR4	Mutation(s): 0 Gene Names: SP_0629
UniProt
Find proteins for A0A0H2UP74 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore A0A0H2UP74 Go to UniProtKB: A0A0H2UP74
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H2UP74
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 M [auth C] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain F [auth B] MOL2 format, chain M [auth C] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain F [auth B] mmCIF format, chain M [auth C] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain F [auth B]	F [auth B], I [auth A], J [auth A], M [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth C] Interactions & Density Focus chain F [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth C]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain G [auth A] SDF format, chain D [auth B] MOL2 format, chain K [auth C] MOL2 format, chain G [auth A] MOL2 format, chain D [auth B] mmCIF format, chain K [auth C] mmCIF format, chain G [auth A] mmCIF format, chain D [auth B]	D [auth B], G [auth A], K [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Focus chain G [auth A] Focus chain K [auth C] Interactions & Density Focus chain D [auth B] Focus chain G [auth A] Focus chain K [auth C]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain H [auth A] SDF format, chain E [auth B] MOL2 format, chain L [auth C] MOL2 format, chain H [auth A] MOL2 format, chain E [auth B] mmCIF format, chain L [auth C] mmCIF format, chain H [auth A] mmCIF format, chain E [auth B]	E [auth B], H [auth A], L [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth B] Focus chain H [auth A] Focus chain L [auth C] Interactions & Density Focus chain E [auth B] Focus chain H [auth A] Focus chain L [auth C]