[English] 日本語
Yorodumi
- PDB-4fiv: FIV PROTEASE COMPLEXED WITH AN INHIBITOR LP-130 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4fiv
TitleFIV PROTEASE COMPLEXED WITH AN INHIBITOR LP-130
ComponentsFELINE IMMUNODEFICIENCY VIRUS PROTEASE
KeywordsASPARTIC PROTEASE / FIV / RETROPEPSIN / RETROVIRUS / CAT
Function / homology
Function and homology information


dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA ...dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / DNA recombination / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / symbiont entry into host cell / magnesium ion binding / proteolysis / DNA binding / zinc ion binding
Similarity search - Function
Deoxyuridine triphosphate nucleotidohydrolase / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Zinc finger integrase-type profile. ...Deoxyuridine triphosphate nucleotidohydrolase / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb 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. / Retropepsin-like catalytic domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H 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 / Pol polyprotein
Similarity search - Component
Biological speciesFeline immunodeficiency 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 15, 1998Processing site: BNL
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650 HELIX DETERMINATION METHOD: TAKEN FROM RELEASED PDB ENTRY 1FIV
Remark 700 SHEET DETERMINATION METHOD: TAKEN FROM RELEASED PDB ENTRY 1FIV

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FELINE IMMUNODEFICIENCY VIRUS PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6382
Polymers12,8431
Non-polymers7951
Water1,65792
1
A: FELINE IMMUNODEFICIENCY VIRUS PROTEASE
hetero molecules

A: FELINE IMMUNODEFICIENCY VIRUS PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2764
Polymers25,6862
Non-polymers1,5902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area6710 Å2
ΔGint-53 kcal/mol
Surface area9470 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)50.650, 50.650, 74.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-201-

LP1

21A-301-

HOH

DetailsTHE AUTHORS NOTE THAT THIS MOLECULE IS ACTIVE AS DIMER

-
Components

#1: Protein FELINE IMMUNODEFICIENCY VIRUS PROTEASE / FIV PR / RETROPEPSIN


Mass: 12842.825 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Feline immunodeficiency virus / Genus: Lentivirus / Production host: Escherichia coli (E. coli) / Strain (production host): PETALUMA
References: UniProt: P16088, UniProt: Q66972*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


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE INHIBITOR LP-130 (1NI 201) IS TWO-FOLD DISORDERED, SO THE TWO ORIENTATIONS FALL ON TOP OF EACH ...THE INHIBITOR LP-130 (1NI 201) IS TWO-FOLD DISORDERED, SO THE TWO ORIENTATIONS FALL ON TOP OF EACH OTHER. SOME ATOMS RELATED BY CRYSTALLOGRAPHIC SYMMETRY MAY BE IN CLOSE CONTACT. THE ALTERNATE LOCATION INDICATOR A HAS BEEN ASSIGNED TO THE DISORDERED INHIBITOR SO THAT THESE ATOMS WOULD NOT BE LISTED AS CLOSE CONTACTS.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 43 %
Crystal growpH: 7.2 / Details: pH 7.2
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
320-25 %MPD1reservoir
450 mMimidazole/HCl1reservoir
51 mMEDTA1reservoir
61 mMdithiothreitol1reservoir
2DMSO1drop

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 2, 1994 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 9993 / % possible obs: 92.3 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.092
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.273 / % possible all: 85.4
Reflection shell
*PLUS
% possible obs: 85.4 %

-
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 1FIV

1fiv


Resolution: 1.8→10 Å / σ(F): 3 /
RfactorNum. reflection
Rwork0.149 -
obs-9085
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms891 0 58 92 1041
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.017
X-RAY DIFFRACTIONp_angle_d0.0460.041
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0480.057
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.9672.4
X-RAY DIFFRACTIONp_mcangle_it2.6333.3
X-RAY DIFFRACTIONp_scbond_it3.9323.7
X-RAY DIFFRACTIONp_scangle_it5.3166.4
X-RAY DIFFRACTIONp_plane_restr0.0170.022
X-RAY DIFFRACTIONp_chiral_restr0.1750.18
X-RAY DIFFRACTIONp_singtor_nbd0.2210.5
X-RAY DIFFRACTIONp_multtor_nbd0.2340.5
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2530.5
X-RAY DIFFRACTIONp_planar_tor3.43.4
X-RAY DIFFRACTIONp_staggered_tor16.413
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor39.720
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROFFT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.149
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