[English] 日本語
Yorodumi
- PDB-2hah: The structure of FIV 12S protease in complex with TL-3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2hah
TitleThe structure of FIV 12S protease in complex with TL-3
ComponentsProtease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / retroviral / protease / aspartyl / feline / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
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-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / DNA recombination / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / 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 / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase (RNA-dependent DNA polymerase) / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Ribonuclease H superfamily / 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
N-[(benzyloxy)carbonyl]-L-alanyl-N-[(1R)-1-benzyl-2-oxoethyl]-L-valinamide / Chem-3TL / Pol polyprotein / Pol polyprotein
Similarity search - Component
Biological speciesFeline immunodeficiency virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHeaslet, H. / Lin, Y.C. / Elder, J.H. / Stout, C.D.
CitationJournal: Retrovirology / Year: 2007
Title: Crystal structure of an FIV/HIV chimeric protease complexed with the broad-based inhibitor, TL-3.
Authors: Heaslet, H. / Lin, Y.C. / Tam, K. / Torbett, B.E. / Elder, J.H. / Stout, C.D.
History
DepositionJun 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Feb 27, 2013Group: Other
Revision 1.4Oct 20, 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 30, 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: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1352
Polymers13,2261
Non-polymers9091
Water2,162120
1
A: Protease
hetero molecules

A: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2714
Polymers26,4522
Non-polymers1,8182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_553x-y,-y,-z-4/31
Buried area5450 Å2
ΔGint-22 kcal/mol
Surface area10220 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)50.324, 50.324, 74.161
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-231-

HOH

-
Components

#1: Protein Protease / Retropepsin


Mass: 13226.226 Da / Num. of mol.: 1 / Fragment: residues 39-154
Mutation: I37V, N55M, M56I, I57G, V59I, G62F, K63I, L97T, I98P, Q99V, P100N, L101I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Feline immunodeficiency virus (isolate Petaluma)
Genus: Lentivirus / Species: Feline immunodeficiency virus / Strain: isolate petaluma / Gene: POL / Plasmid: pET-21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS
References: UniProt: P16088, UniProt: Q66972*PLUS, HIV-1 retropepsin
#2: Chemical ChemComp-3TL / benzyl [(1S,4S,7S,8R,9R,10S,13S,16S)-7,10-dibenzyl-8,9-dihydroxy-1,16-dimethyl-4,13-bis(1-methylethyl)-2,5,12,15,18-pentaoxo-20-phenyl-19-oxa-3,6,11,14,17-pentaazaicos-1-yl]carbamate / TL-3, C2 symmetric inhibitor


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 909.077 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C50H64N6O10
References: N-[(benzyloxy)carbonyl]-L-alanyl-N-[(1R)-1-benzyl-2-oxoethyl]-L-valinamide
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE INHIBITOR IS A C2 SYMMETRIC HIV PROTEASE

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 39.97 %
Crystal growTemperature: 281.16 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM Hepes, 2.5M LiCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 281.16K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.97944 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 18, 2006
Details: Double-crystal monochromator, 1m long Rh coated bent cylindrical mirror for horizontal and vertical focusing
RadiationMonochromator: Double crystal, parallel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97944 Å / Relative weight: 1
ReflectionResolution: 1.7→74 Å / Num. all: 12484 / Num. obs: 12440 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Redundancy: 6.2 % / Rmerge(I) obs: 0.07
Reflection shellHighest resolution: 1.7 Å / Redundancy: 6 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 2.6 / Num. unique all: 5451 / % possible all: 99

-
Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT2data extraction
Blu-Icedata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 5FIV

5fiv


Resolution: 1.7→74 Å / FOM work R set: 0.874 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.233 627 5 %Random
Rwork0.184 ---
all0.184 12424 --
obs0.233 12396 99.6 %-
Solvent computationBsol: 60.962 Å2
Displacement parametersBiso mean: 24.431 Å2
Baniso -1Baniso -2Baniso -3
1-0.375 Å20.61 Å20 Å2
2--0.375 Å20 Å2
3----0.751 Å2
Refinement stepCycle: LAST / Resolution: 1.7→74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms892 0 33 120 1045
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.1661.5
X-RAY DIFFRACTIONc_scbond_it2.1122
X-RAY DIFFRACTIONc_mcangle_it1.7722
X-RAY DIFFRACTIONc_scangle_it3.0552.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
1.7-1.750.265560.2519601016
1.75-1.810.257410.2319671008
1.81-1.870.335490.2219721021
1.87-1.950.269610.2289541015
1.95-2.030.245440.1869751019
2.03-2.140.204480.1829701018
2.14-2.280.241500.189831033
2.28-2.450.261450.29761021
2.45-2.70.218600.169681028
2.7-3.090.241590.19310041063
3.09-3.890.21610.1629991060
3.89-740.22530.17510411094
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2int.par
X-RAY DIFFRACTION3water_rep.param

+
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