[English] 日本語
Yorodumi
- PDB-29sb: Solution structure of inhibitor (6-NBT)-bound de novo designed Ke... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 29sb
TitleSolution structure of inhibitor (6-NBT)-bound de novo designed Kemp eliminase KABLE2.5.
ComponentsKABLE2.5
KeywordsDE NOVO PROTEIN / Helical bundle / Catalysis
Function / homology6-NITROBENZOTRIAZOLE
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing / torsion angle dynamics
AuthorsVolkov, A.N. / Mouloud, W.E.Y. / Bhattacharya, S.
Funding support United States, 4items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB- 2306190 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122603 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM145238 United States
Damon Runyon Cancer Research FoundationDRG-2522-24 United States
CitationJournal: To Be Published
Title: Solution structure of inhibitor (6-NBT)-bound de novo designed Kemp eliminase KABLE2.5.
Authors: Volkov, A.N. / Bhattacharya, S.
History
DepositionApr 2, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: KABLE2.5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8502
Polymers14,6861
Non-polymers1641
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein KABLE2.5


Mass: 14685.769 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-6NT / 6-NITROBENZOTRIAZOLE


Mass: 164.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H4N4O2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic13D HN(CA)CB
141isotropic13D HN(COCA)CB
151isotropic13D HNCO
161isotropic13D HN(CA)CO
171isotropic13D HBHA(CO)NH
181isotropic13D (H)CCH-TOCSY
191isotropic12D 1H-13C HSQC aromatic
1101isotropic13D 1H-15N NOESY
1111isotropic13D 1H-13C NOESY aliphatic
1121isotropic12D (HB)CB(CGCD)HD
1131isotropic12D (HB)CB(CGCDCE)HE
1141isotropic12D CB-CG
1151isotropic13D 1H-13C NOESY aromatic

-
Sample preparation

DetailsType: solution
Contents: 2 mM [U-100% 13C; U-100% 15N] KABLE2.5, 100 mM sodium chloride, 20 mM HEPES, 10 % [U-2H] D2O, 90 % H2O, 8 mM 6-NBT, 7.4 % v/v [U-2H] CD3CN, 90% H2O/10% D2O
Label: sample_1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMKABLE2.5[U-100% 13C; U-100% 15N]1
100 mMsodium chloridenatural abundance1
20 mMHEPESnatural abundance1
10 %D2O[U-2H]1
90 %H2Onatural abundance1
8 mM6-NBTnatural abundance1
7.4 % v/vCD3CN[U-2H]1
Sample conditionsIonic strength: 118 mM / Label: sample_conditions_1 / pH: 6.9 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.7Bruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
CcpNmr AnalysisCCPNdata analysis
TopSpinBruker Biospinprocessing
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
Refinement
MethodSoftware ordinal
simulated annealing8
torsion angle dynamics9
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more