8JSU | pdb_00008jsu

The crystal structure of TvaE in complex with TvaLP

PDB DOI: https://doi.org/10.2210/pdb8JSU/pdb

Classification: LYASE
Organism(s): Streptomyces sp. NRRL S-87
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-06-20 Released: 2025-09-03
Deposition Author(s): Li, M., Pan, L.F.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.44 Å
R-Value Free:
0.197 (Depositor), 0.198 (DCC)
R-Value Work:
0.173 (Depositor), 0.173 (DCC)
R-Value Observed:
0.174 (Depositor)

Starting Model: in silico
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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

Pseudokinases Can Catalyze Peptide Cyclization through Thioether Crosslinking

Li, M., Pan, L.F.

(2025) Nat Chem

Macromolecule Content

Total Structure Weight: 76.01 kDa
Atom Count: 6,155
Modeled Residue Count: 702
Deposited Residue Count: 714
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TvaLP	A, C	42	Streptomyces sp. NRRL S-87	Mutation(s): 0
UniProt
Find proteins for A0A1R1S5P8 (Streptomyces sparsogenes DSM 40356) Explore A0A1R1S5P8 Go to UniProtKB: A0A1R1S5P8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1R1S5P8
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TvaE	B, D	315	Streptomyces sp. NRRL S-87	Mutation(s): 0
UniProt
Find proteins for A0A7W9H480 (Streptomyces caelestis) Explore A0A7W9H480 Go to UniProtKB: A0A7W9H480
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A7W9H480
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG (Subject of Investigation/LOI) Query on PEG Download:Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain I [auth B] MOL2 format, chain O [auth D] MOL2 format, chain I [auth B] mmCIF format, chain O [auth D] mmCIF format, chain I [auth B]	I [auth B], O [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain O [auth D] Interactions & Density Focus chain I [auth B] Focus chain O [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain K [auth B] SDF format, chain J [auth B] MOL2 format, chain N [auth D] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] mmCIF format, chain N [auth D] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B]	J [auth B], K [auth B], N [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth D] Interactions & Density Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth D]
BR Query on BR Download:Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain G [auth B] SDF format, chain F [auth B] MOL2 format, chain M [auth D] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] mmCIF format, chain M [auth D] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B]	F [auth B], G [auth B], M [auth D]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M		Interactions Focus chain F [auth B] Focus chain G [auth B] Focus chain M [auth D] Interactions & Density Focus chain F [auth B] Focus chain G [auth B] Focus chain M [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain E [auth B] MOL2 format, chain L [auth D] MOL2 format, chain E [auth B] mmCIF format, chain L [auth D] mmCIF format, chain E [auth B]	E [auth B], L [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain L [auth D] Interactions & Density Focus chain E [auth B] Focus chain L [auth D]