9IV0 | pdb_00009iv0

Crystal Structure of Sortase E mutant Y128F from Thermobifida fusca

PDB DOI: https://doi.org/10.2210/pdb9IV0/pdb

Classification: HYDROLASE
Organism(s): Thermobifida fusca YX
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-07-22 Released: 2025-07-23
Deposition Author(s): Sharma, V., Murmu, S., Roy, R.P., Krishnan, V.
Funding Organization(s): Department of Biotechnology (DBT, India)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free:
0.214 (Depositor), 0.225 (DCC)
R-Value Work:
0.177 (Depositor), 0.188 (DCC)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure Analysis of Sortase E from Thermobifida fusca

Sharma, V., Murmu, S., Roy, R.P., Krishnan, V.

To be published.

Macromolecule Content

Total Structure Weight: 41.13 kDa
Atom Count: 2,887
Modeled Residue Count: 344
Deposited Residue Count: 362
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidase C60, sortase A and B	A, B	181	Thermobifida fusca YX	Mutation(s): 1 Gene Names: Tfu_2383
UniProt
Find proteins for A0AA97LU39 (Thermobifida halotolerans) Explore A0AA97LU39 Go to UniProtKB: A0AA97LU39
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0AA97LU39
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL (Subject of Investigation/LOI) Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain G [auth A] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], G [auth A], K [auth B], L [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B]
CL (Subject of Investigation/LOI) Query on CL Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain C [auth A] MOL2 format, chain I [auth B] MOL2 format, chain C [auth A] mmCIF format, chain I [auth B] mmCIF format, chain C [auth A]	C [auth A], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]
NA (Subject of Investigation/LOI) Query on NA Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain H [auth B] SDF format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain H [auth B] MOL2 format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain H [auth B] mmCIF format, chain D [auth A]	D [auth A], H [auth B], J [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B] Focus chain J [auth B]