9G48 | pdb_00009g48

Staphylococcus aureus MazF in complex with Nanobody 6

PDB DOI: https://doi.org/10.2210/pdb9G48/pdb

Classification: TOXIN
Organism(s): Staphylococcus aureus, Lama glama
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-07-15 Released: 2024-07-24
Deposition Author(s): Zorzini, V., Haesaerts, S., Loris, R.
Funding Organization(s): Vrije Universiteit Brussel

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.14 Å
R-Value Free:
0.245 (Depositor), 0.250 (DCC)
R-Value Work:
0.216 (Depositor), 0.220 (DCC)
R-Value Observed:
0.218 (Depositor)

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Nanobody-mediated activation and inhibition of Staphylococcus aureus MazF

Prolic-Kalinsek, M., Zorzini, V., Haesaerts, S., De Bruyn, P., Loris, R.

To be published.

Macromolecule Content

Total Structure Weight: 61.2 kDa
Atom Count: 3,857
Modeled Residue Count: 492
Deposited Residue Count: 542
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoribonuclease MazF	A, B	133	Staphylococcus aureus	Mutation(s): 0 Gene Names: mazF, SA1873 EC: 3.1
UniProt
Find proteins for Q2FWI8 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FWI8 Go to UniProtKB: Q2FWI8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2FWI8
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody 6	C, D	138	Lama glama	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
PG0 Query on PG0 Download Ideal Coordinates CCD File SDF format, chain K [auth D] MOL2 format, chain K [auth D] mmCIF format, chain K [auth D]	K [auth D]	2-(2-METHOXYETHOXY)ETHANOL C₅ H₁₂ O₃ SBASXUCJHJRPEV-UHFFFAOYSA-N		Interactions Focus chain K [auth D] Interactions & Density Focus chain K [auth D]
CD Query on CD Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth D] SDF format, chain J [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth D] MOL2 format, chain J [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth D] mmCIF format, chain J [auth D]	E [auth A], F [auth A], H [auth B], I [auth D], J [auth D]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth D] Focus chain J [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth D] Focus chain J [auth D]