37LZ | pdb_000037lz

Structure of KomA in complex with pentostatin

PDB DOI: https://doi.org/10.2210/pdb37LZ/pdb

Classification: HYDROLASE
Organism(s): Escherichia coli
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2026-07-25 Released: 2026-11-11
Deposition Author(s): Zhou, J., Horton, J.R., Cheng, X.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), Cancer Prevention and Research Institute of Texas (CPRIT)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.267 (Depositor), 0.267 (DCC)
R-Value Work:
0.225 (Depositor), 0.225 (DCC)
R-Value Observed:
0.227 (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

Structure of KomA in complex with pentostatin

Zhou, J., Horton, J.R., Cheng, X.

To be published.

Macromolecule Content

Total Structure Weight: 74.75 kDa
Atom Count: 5,265
Modeled Residue Count: 653
Deposited Residue Count: 656
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
KomA	A, B	328	Escherichia coli	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DCF (Subject of Investigation/LOI) Query on DCF Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain N [auth B] MOL2 format, chain D [auth A] MOL2 format, chain N [auth B] mmCIF format, chain D [auth A] mmCIF format, chain N [auth B]	D [auth A], N [auth B]	2'-DEOXYCOFORMYCIN C₁₁ H₁₆ N₄ O₄ FPVKHBSQESCIEP-JQCXWYLXSA-N		Interactions Focus chain D [auth A] Focus chain N [auth B] Interactions & Density Focus chain D [auth A] Focus chain N [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain Q [auth B] MOL2 format, chain M [auth A] MOL2 format, chain Q [auth B] mmCIF format, chain M [auth A] mmCIF format, chain Q [auth B]	M [auth A], Q [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain Q [auth B] Interactions & Density Focus chain M [auth A] Focus chain Q [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B]	C [auth A] E [auth A] F [auth A] G [auth A] H [auth A] C [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], O [auth B], P [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.267 (Depositor), 0.267 (DCC)
R-Value Work: 0.225 (Depositor), 0.225 (DCC)
R-Value Observed: 0.227 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.058	α = 90
b = 127.386	β = 90.16
c = 79.542	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-11-11

Deposition Author(s):

Zhou, J.

Horton, J.R.

Cheng, X.

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R35GM134744
Cancer Prevention and Research Institute of Texas (CPRIT)	United States	RR160029