[English] 日本語
Yorodumi
- PDB-7up3: NDM1-inhibitor co-structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7up3
TitleNDM1-inhibitor co-structure
ComponentsMetallo beta-lactamase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Metallo-beta-lactamase inhibitor / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


beta-lactamase activity / metal ion binding
Similarity search - Function
: / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Chem-NZ0 / NDM-1
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4 Å
AuthorsScapin, G. / Fischmann, T.O.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2022
Title: Rapid Evolution of a Fragment-like Molecule to Pan-Metallo-Beta-Lactamase Inhibitors: Initial Leads toward Clinical Candidates.
Authors: Mandal, M. / Xiao, L. / Pan, W. / Scapin, G. / Li, G. / Tang, H. / Yang, S.W. / Pan, J. / Root, Y. / de Jesus, R.K. / Yang, C. / Prosise, W. / Dayananth, P. / Mirza, A. / Therien, A.G. / ...Authors: Mandal, M. / Xiao, L. / Pan, W. / Scapin, G. / Li, G. / Tang, H. / Yang, S.W. / Pan, J. / Root, Y. / de Jesus, R.K. / Yang, C. / Prosise, W. / Dayananth, P. / Mirza, A. / Therien, A.G. / Young, K. / Flattery, A. / Garlisi, C. / Zhang, R. / Chu, D. / Sheth, P. / Chu, I. / Wu, J. / Markgraf, C. / Kim, H.Y. / Painter, R. / Mayhood, T.W. / DiNunzio, E. / Wyss, D.F. / Buevich, A.V. / Fischmann, T. / Pasternak, A. / Dong, S. / Hicks, J.D. / Villafania, A. / Liang, L. / Murgolo, N. / Black, T. / Hagmann, W.K. / Tata, J. / Parmee, E.R. / Weber, A.E. / Su, J. / Tang, H.
History
DepositionApr 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Metallo beta-lactamase
B: Metallo beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,29713
Polymers52,5892
Non-polymers1,70811
Water5,603311
1
A: Metallo beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0306
Polymers26,2951
Non-polymers7355
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metallo beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2687
Polymers26,2951
Non-polymers9736
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.564, 73.913, 77.325
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Metallo beta-lactamase / Metallo-beta-lactamase NDM-1 / Metallo-beta-lactamase / NDM-1 / Metallobetalactamase NDM-1 / NDM1 ...Metallo-beta-lactamase NDM-1 / Metallo-beta-lactamase / NDM-1 / Metallobetalactamase NDM-1 / NDM1 metallo-beta-lactamase / New Delhi Metallo carbapenemase-1 / New Delhi metallo beta lactamase 1 / New Delhi metallo-beta-lactamase NDM-1 / Subclass B1 metallo-beta-lactamase NDM-1


Mass: 26294.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: blaNDM-1, bla NDM-1, blaNDM1, NDM-1, D647_p47098, DDJ63_29735, EC13450_007, NCTC13443_00040, p2146_00143, pCRE380_21, pN11x00042NDM_090, pNDM-SX04_5, pNDM10469_138, SAMEA3499901_05193, TR3_031, TR4_031
Production host: Escherichia coli (E. coli) / References: UniProt: E9NWK5

-
Non-polymers , 5 types, 322 molecules

#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-NZ0 / (3P)-4-[4-(hydroxymethyl)phenyl]-3-(2H-tetrazol-5-yl)pyridine-2-sulfonamide


Mass: 332.338 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H12N6O3S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.89 Å3/Da / Density % sol: 34.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M ammonium acetate 1.0 mM TCEP 3.0 mM cadmium sulfate 0.1 M HEPES pH 7.0 25.0 w/v polyethylene glycol 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.113→134.175 Å / Num. all: 163291 / Num. obs: 163291 / % possible obs: 100 % / Redundancy: 12.8 % / Biso Wilson estimate: 17.2 Å2 / Rpim(I) all: 0.029 / Rrim(I) all: 0.105 / Rsym value: 0.094 / Net I/av σ(I): 5.9 / Net I/σ(I): 18 / Num. measured all: 2088252
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value
1.113-1.1712.60.5621.4235380.1710.6120.562
1.17-1.2412.20.4471.7223770.1390.4890.447
1.24-1.33130.3392.2210230.1020.3690.339
1.33-1.4412.70.243.1196160.0730.2630.24
1.44-1.5713.10.1634.6181130.050.180.163
1.57-1.7613.40.1146.5164180.0350.1270.114
1.76-2.0312.70.0779.1145350.0250.0880.077
2.03-2.4913.20.05911.4123700.0190.0680.059
2.49-3.5212.50.04812.597180.0160.0560.048
3.52-134.17512.50.04413.455830.0140.050.044

-
Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSdata reduction
SCALA3.3.20data scaling
PDB_EXTRACT3.27data extraction
BUSTERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3ZR9

3zr9


Resolution: 1.4→31.72 Å / Cor.coef. Fo:Fc: 0.9434 / Cor.coef. Fo:Fc free: 0.9418 / SU R Cruickshank DPI: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.065 / SU Rfree Blow DPI: 0.061 / SU Rfree Cruickshank DPI: 0.06
RfactorNum. reflection% reflectionSelection details
Rfree0.1899 3839 5.02 %RANDOM
Rwork0.1803 ---
obs0.1808 76421 96.65 %-
Displacement parametersBiso max: 106.58 Å2 / Biso mean: 23.06 Å2 / Biso min: 10.04 Å2
Baniso -1Baniso -2Baniso -3
1--4.8733 Å20 Å20 Å2
2--3.8472 Å20 Å2
3---1.0261 Å2
Refine analyzeLuzzati coordinate error obs: 0.171 Å
Refinement stepCycle: final / Resolution: 1.4→31.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3381 0 68 311 3760
Biso mean--30.13 28.95 -
Num. residues----458
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1138SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes91HARMONIC2
X-RAY DIFFRACTIONt_gen_planes540HARMONIC5
X-RAY DIFFRACTIONt_it3536HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion465SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4312SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3536HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4825HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion4.13
X-RAY DIFFRACTIONt_other_torsion16.09
LS refinement shellResolution: 1.4→1.44 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.1977 255 5.02 %
Rwork0.1932 4827 -
all0.1934 5082 -
obs--96.65 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.66390.0749-0.02683.3249-0.3570.40840.0219-0.012-0.09150.4622-0.0708-0.10950.00480.02440.0489-0.0101-0.0097-0.0221-0.06990.004-0.0869-16.18323.3328-5.7768
20.3459-0.08860.10291.5731-0.00570.6734-0.00840.01580.04390.0388-0.0191-0.0282-0.04050.00520.0275-0.03010.0021-0.0029-0.01180.0076-0.0468-18.821535.6515-18.0533
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A42 - 269
2X-RAY DIFFRACTION2{ B|* }B42 - 270

+
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