7FD6 | pdb_00007fd6

Crystal structure of SmChiA in complex with 6a

PDB DOI: https://doi.org/10.2210/pdb7FD6/pdb

Classification: HYDROLASE
Organism(s): Serratia marcescens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-07-16 Released: 2022-07-20
Deposition Author(s): Xi, J., Qing, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free:
0.190 (Depositor), 0.190 (DCC)
R-Value Work:
0.166 (Depositor), 0.170 (DCC)
R-Value Observed:
0.167 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Discovery of Conformation Constrained Tetracyclic Compounds as potent Chitinase OfChi-h inhibitor with novel binding mode

Pengtao, Y., Xi, J.

To be published.

Macromolecule Content

Total Structure Weight: 60.13 kDa
Atom Count: 4,902
Modeled Residue Count: 538
Deposited Residue Count: 548
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chitinase A	A	548	Serratia marcescens	Mutation(s): 0 Gene Names: chiA, PWN146_04604 EC: 3.2.1.14
UniProt
Find proteins for P07254 (Serratia marcescens) Explore P07254 Go to UniProtKB: P07254
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07254
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4QU (Subject of Investigation/LOI) Query on 4QU Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	11-methyl-3-(pyridin-3-ylmethyl)-4H-pyrimido[5'',4'':5',6']pyrido[2',3':4,5]pyrimido[1,2-b]pyridine-4,6(3H)-dione C₂₀ H₁₄ N₆ O₂ BFJYZGRLIJMXES-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free: 0.190 (Depositor), 0.190 (DCC)
R-Value Work: 0.166 (Depositor), 0.170 (DCC)
R-Value Observed: 0.167 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.525	α = 90
b = 202.186	β = 90
c = 59.43	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2022-07-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2022-07-20
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description
Version 1.2: 2024-11-20
Changes: Structure summary

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.