9CGL

Pikromycin Thioesterase Doubly Protected DAP

PDB DOI: https://doi.org/10.2210/pdb9CGL/pdb

Classification: HYDROLASE
Organism(s): Streptomyces venezuelae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-06-29 Released: 2024-09-18
Deposition Author(s): McCullough, T.M., Smith, J.L.
Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.233
R-Value Work: 0.181
R-Value Observed: 0.183

Starting Model: experimental
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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

Substrate Trapping in Polyketide Synthase Thioesterase Domains: Structural Basis for Macrolactone Formation

McCullough, T.M., Choudhary, V., Akey, D.L., Skiba, M.A., Bernard, S.M., Kittendorf, J.D., Schmidt, J.J., Sherman, D.H., Smith, J.L.

(2024) ACS Catal 14

DOI: https://doi.org/10.1021/acscatal.4c03637

Macromolecule Content

Total Structure Weight: 62.33 kDa
Atom Count: 4,410
Modelled Residue Count: 554
Deposited Residue Count: 580
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Narbonolide/10-deoxymethynolide synthase PikA4, module 6	A, B	290	Streptomyces venezuelae	Mutation(s): 1 Gene Names: pikAIV EC: 2.3.1.239 (PDB Primary Data), 2.3.1.240 (PDB Primary Data)
UniProt
Find proteins for Q9ZGI2 (Streptomyces venezuelae) Explore Q9ZGI2 Go to UniProtKB: Q9ZGI2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9ZGI2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1AWE (Subject of Investigation/LOI) Query on A1AWE Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	2-{[(1R)-1-(6-nitro-2H-1,3-benzodioxol-5-yl)ethyl]sulfanyl}ethyl formate C₁₂ H₁₃ N O₆ S OAPSBASJSSKBSD-MRVPVSSYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DPP Query on DPP	A, B	L-PEPTIDE LINKING	C₃ H₈ N₂ O₂		ALA

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.233
R-Value Work: 0.181
R-Value Observed: 0.183
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.124	α = 90
b = 105.858	β = 90
c = 114.533	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-09-18

Deposition Author(s):

McCullough, T.M.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	DK042303

Revision History (Full details and data files)

Version 1.0: 2024-09-18
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.