[English] 日本語
Yorodumi
- PDB-2fmb: EIAV PROTEASE COMPLEXED WITH AN INHIBITOR LP-130 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2fmb
TitleEIAV PROTEASE COMPLEXED WITH AN INHIBITOR LP-130
ComponentsEQUINE INFECTIOUS ANEMIA VIRUS PROTEASE
KeywordsASPARTIC PROTEASE / RETROPEPSIN / RETROVIRUS / EIAV / HORSE
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases ...Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / DNA recombination / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / symbiont entry into host cell / proteolysis / DNA binding / zinc ion binding / metal ion binding
Similarity search - Function
dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. ...dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Cathepsin D, subunit A; domain 1 / Acid Proteases / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-LP1 / Pol polyprotein / Protease
Similarity search - Component
Biological speciesEquine infectious anemia virus
MethodX-RAY DIFFRACTION / RIGID BODY REFINEMENT / Resolution: 1.8 Å
AuthorsKervinen, J. / Lubkowski, J. / Zdanov, A. / Wlodawer, A. / Gustchina, A.
CitationJournal: Protein Sci. / Year: 1998
Title: Toward a universal inhibitor of retroviral proteases: comparative analysis of the interactions of LP-130 complexed with proteases from HIV-1, FIV, and EIAV.
Authors: Kervinen, J. / Lubkowski, J. / Zdanov, A. / Bhatt, D. / Dunn, B.M. / Hui, K.Y. / Powell, D.J. / Kay, J. / Wlodawer, A. / Gustchina, A.
History
DepositionJul 13, 1998Processing site: BNL
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: EQUINE INFECTIOUS ANEMIA VIRUS PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1872
Polymers11,3921
Non-polymers7951
Water1,802100
1
A: EQUINE INFECTIOUS ANEMIA VIRUS PROTEASE
hetero molecules

A: EQUINE INFECTIOUS ANEMIA VIRUS PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3744
Polymers22,7852
Non-polymers1,5902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6500 Å2
ΔGint-45 kcal/mol
Surface area9370 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)42.650, 45.360, 56.760
Angle α, β, γ (deg.)90.00, 110.36, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-301-

HOH

DetailsTHIS FILE CONTAINS ONLY A MONOMER, WHILE THE ACTIVE ENZYME IS A DIMER. IN ORDER TO CREATE A DIMERIC MOLECULE, CRYSTALLOGRAPHIC COORDINATES NEED TO BE TRANSFORMED TO (-X), Y, (-Z). THE TWO ORIENTATIONS OF THE INHIBITOR CREATED IN THAT MANNER OVERLAP, WITH COMPLETE SUPERPOSITION AT THE PERIPHERY AND SOME DEVIATION IN THE CENTER. RESIDUES 56 - 58 HAVE BEEN MODELED WITH TWO ORIENTATIONS OF THEIR MAIN CHAINS, SINCE THEY FORM ALTERNATE HYDROGEN BONDS, DUE TO THE SAME DISORDER PHENOMENON.

-
Components

#1: Protein EQUINE INFECTIOUS ANEMIA VIRUS PROTEASE / EIAV PR / RETROPEPSIN


Mass: 11392.265 Da / Num. of mol.: 1 / Mutation: I54G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equine infectious anemia virus / Genus: Lentivirus / Production host: Escherichia coli (E. coli) / Strain (production host): PV
References: UniProt: P32542, UniProt: Q66729*PLUS, HIV-1 retropepsin
#2: Chemical ChemComp-LP1 / 4-[2-(2-ACETYLAMINO-3-NAPHTALEN-1-YL-PROPIONYLAMINO)-4-METHYL-PENTANOYLAMINO]-3-HYDROXY-6-METHYL-HEPTANOIC ACID [1-(1-CARBAMOYL-2-NAPHTHALEN-1-YL-ETHYLCARBAMOYL)-PROPYL]-AMIDE


Mass: 794.978 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C45H58N6O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsKI VALUE OF LP-130 FOR EIAV PR IS 2 NM

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.54 %
Crystal growpH: 4.6 / Details: pH 4.6
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
320 %PEG40001reservoir
425 mMsodium acetate1reservoir
50.45 Mammonium sulfate1reservoir
66 %DMSO1reservoir
70.1 %sodium azide1reservoir
2DMSO1drop

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Sep 18, 1996 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 8666 / % possible obs: 90.9 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.049
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.3 / % possible all: 81.4
Reflection shell
*PLUS
% possible obs: 91.4 %

-
Processing

Software
NameClassification
X-PLORmodel building
PROFFTrefinement
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: RIGID BODY REFINEMENT
Starting model: PDB ENTRY 1FMB

1fmb


Resolution: 1.8→10 Å / σ(F): 3
RfactorNum. reflection% reflection
Rwork0.143 --
obs-8460 90.9 %
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms791 0 58 100 949
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.017
X-RAY DIFFRACTIONp_angle_d0.0450.044
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0440.059
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.9162.5
X-RAY DIFFRACTIONp_mcangle_it2.5673.5
X-RAY DIFFRACTIONp_scbond_it3.724
X-RAY DIFFRACTIONp_scangle_it5.3287
X-RAY DIFFRACTIONp_plane_restr0.0180.022
X-RAY DIFFRACTIONp_chiral_restr0.1770.18
X-RAY DIFFRACTIONp_singtor_nbd0.2070.5
X-RAY DIFFRACTIONp_multtor_nbd0.450.5
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.3820.5
X-RAY DIFFRACTIONp_planar_tor3.43.5
X-RAY DIFFRACTIONp_staggered_tor19.114
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor32.412
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROFFT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.143
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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