3HH6 | pdb_00003hh6

New azaborine compounds bind to the T4 lysozyme L99A cavity -ethylbenzene as control

PDB DOI: https://doi.org/10.2210/pdb3HH6/pdb

Classification: HYDROLASE
Organism(s): Tequatrovirus T4
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2009-05-14 Released: 2009-10-13
Deposition Author(s): Liu, L., Matthews, B.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free:
0.182 (Depositor), 0.181 (DCC)
R-Value Work:
0.162 (Depositor), 0.162 (DCC)
R-Value Observed:
0.163 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Boron mimetics: 1,2-dihydro-1,2-azaborines bind inside a nonpolar cavity of T4 lysozyme.

Liu, L., Marwitz, A.J., Matthews, B.W., Liu, S.Y.

(2009) Angew Chem Int Ed Engl 48: 6817-6819

PubMed: 19688806 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/anie.200903390
Primary Citation Related Structures:
3HH3, 3HH4, 3HH5, 3HH6

Organizational Affiliation

Institute of Molecular Biology and Department of Physics, University of Oregon, Eugene, OR 97403-1253, USA.

Macromolecule Content

Total Structure Weight: 19.1 kDa
Atom Count: 1,729
Modeled Residue Count: 163
Deposited Residue Count: 164
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme	A	164	Tequatrovirus T4	Mutation(s): 3 Gene Names: E EC: 3.2.1.17
UniProt
Find proteins for P00720 (Enterobacteria phage T4) Explore P00720 Go to UniProtKB: P00720
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00720
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HED Query on HED Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	2-HYDROXYETHYL DISULFIDE C₄ H₁₀ O₂ S₂ KYNFOMQIXZUKRK-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
PYJ Query on PYJ Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	PHENYLETHANE C₈ H₁₀ YNQLUTRBYVCPMQ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.182 (Depositor), 0.181 (DCC)
R-Value Work: 0.162 (Depositor), 0.162 (DCC)
R-Value Observed: 0.163 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.799	α = 90
b = 59.799	β = 90
c = 95.568	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-10-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-10-13
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2013-12-25
Changes: Non-polymer description
Version 1.3: 2017-11-01
Changes: Refinement description
Version 1.4: 2021-10-13
Changes: Database references, Derived calculations
Version 1.5: 2023-09-06
Changes: Data collection, Refinement description

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