9G7K

Staphylococcus aureus MazF in complex with Nanobody 12

PDB DOI: https://doi.org/10.2210/pdb9G7K/pdb

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

Deposited: 2024-07-21 Released: 2024-07-31
Deposition Author(s): Zorzini, V., Haesaerts, S., Loris, R.
Funding Organization(s): Vrije Universiteit Brussel

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free: 0.234
R-Value Work: 0.189
R-Value Observed: 0.191

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 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: 122.33 kDa
Atom Count: 8,126
Modelled Residue Count: 993
Deposited Residue Count: 1,076
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoribonuclease MazF	A, B, E, F	133	Staphylococcus aureus	Mutation(s): 0 Gene Names: mazF, SA1873 EC: 3.1
UniProt
Find proteins for Q7A4G9 (Staphylococcus aureus (strain N315)) Explore Q7A4G9 Go to UniProtKB: Q7A4G9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7A4G9
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 12	C, D, G, H	136	Lama glama	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain FA [auth G] SDF format, chain GA [auth G] SDF format, chain HA [auth G] SDF format, chain IA [auth H] SDF format, chain J [auth A] SDF format, chain JA [auth H] SDF format, chain KA [auth H] SDF format, chain L [auth B] SDF format, chain LA [auth H] SDF format, chain M [auth B] SDF format, chain MA [auth H] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain V [auth E] SDF format, chain W [auth E] SDF format, chain X [auth E] SDF format, chain Z [auth F] MOL2 format, chain FA [auth G] MOL2 format, chain GA [auth G] MOL2 format, chain HA [auth G] MOL2 format, chain IA [auth H] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth H] MOL2 format, chain KA [auth H] MOL2 format, chain L [auth B] MOL2 format, chain LA [auth H] MOL2 format, chain M [auth B] MOL2 format, chain MA [auth H] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain V [auth E] MOL2 format, chain W [auth E] MOL2 format, chain X [auth E] MOL2 format, chain Z [auth F]	FA [auth G] GA [auth G] HA [auth G] IA [auth H] J [auth A] FA [auth G], GA [auth G], HA [auth G], IA [auth H], J [auth A], JA [auth H], KA [auth H], L [auth B], LA [auth H], M [auth B], MA [auth H], N [auth B], O [auth B], P [auth C], Q [auth C], R [auth C], V [auth E], W [auth E], X [auth E], Z [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain FA [auth G] Focus chain GA [auth G] Focus chain HA [auth G] Focus chain IA [auth H] Focus chain J [auth A] Focus chain JA [auth H] Focus chain KA [auth H] Focus chain L [auth B] Focus chain LA [auth H] Focus chain M [auth B] Focus chain MA [auth H] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain V [auth E] Focus chain W [auth E] Focus chain X [auth E] Focus chain Z [auth F]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain BA [auth G] SDF format, chain CA [auth G] SDF format, chain DA [auth G] SDF format, chain EA [auth G] SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain S [auth D] SDF format, chain T [auth D] SDF format, chain U [auth E] SDF format, chain Y [auth F] MOL2 format, chain AA [auth G] MOL2 format, chain BA [auth G] MOL2 format, chain CA [auth G] MOL2 format, chain DA [auth G] MOL2 format, chain EA [auth G] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain U [auth E] MOL2 format, chain Y [auth F]	AA [auth G] BA [auth G] CA [auth G] DA [auth G] EA [auth G] AA [auth G], BA [auth G], CA [auth G], DA [auth G], EA [auth G], I [auth A], K [auth B], S [auth D], T [auth D], U [auth E], Y [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth G] Focus chain BA [auth G] Focus chain CA [auth G] Focus chain DA [auth G] Focus chain EA [auth G] Focus chain I [auth A] Focus chain K [auth B] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth E] Focus chain Y [auth F]