[English] 日本語
Yorodumi
- PDB-2qhy: Crystal Structure of protease inhibitor, MIT-1-AC86 in complex wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2qhy
TitleCrystal Structure of protease inhibitor, MIT-1-AC86 in complex with wild type HIV-1 protease
ComponentsProtease
KeywordsHYDROLASE / Drug design / HIV-1 protease / protease inhibitors
Function / homology
Function and homology information


HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane
Similarity search - Function
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 ...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. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / 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 / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Cathepsin D, subunit A; domain 1 / Acid Proteases / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / 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
ACETATE ION / Chem-MZ1 / PHOSPHATE ION / Protease / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSchiffer, C.A. / Nalam, M.N.L.
CitationJournal: J.Am.Chem.Soc. / Year: 2008
Title: HIV-1 protease inhibitors from inverse design in the substrate envelope exhibit subnanomolar binding to drug-resistant variants.
Authors: Altman, M.D. / Ali, A. / Reddy, G.S. / Nalam, M.N. / Anjum, S.G. / Cao, H. / Chellappan, S. / Kairys, V. / Fernandes, M.X. / Gilson, M.K. / Schiffer, C.A. / Rana, T.M. / Tidor, B.
History
DepositionJul 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Refinement description / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Oct 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 1.4Aug 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
B: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,83111
Polymers21,6322
Non-polymers1,2009
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-49 kcal/mol
Surface area9370 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)50.670, 57.981, 61.541
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Protease /


Mass: 10815.790 Da / Num. of mol.: 2 / Mutation: Q7K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: SF2 / Gene: pol / Plasmid: PXC35 / Production host: Escherichia coli (E. coli) / Strain (production host): TAP56 / References: UniProt: O38732, UniProt: P03369*PLUS
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-MZ1 / N~2~-ACETYL-N-[(1S,2R)-1-BENZYL-2-HYDROXY-3-{(2-THIENYLMETHYL)[(2,4,5-TRIFLUOROPHENYL)SULFONYL]AMINO}PROPYL]-L-ALANINAMIDE


Mass: 583.643 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H28F3N3O5S2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 126 mM Sodium Phosphate, 63 mM sodium citrate, 24-29% ammonium sulphate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 23, 2005 / Details: osmic mirrors
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 15580 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.047 / Rsym value: 4.7 / Net I/σ(I): 10.9

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1F7A

1f7a


Resolution: 1.85→42.18 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.311 / SU ML: 0.083 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.147 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19748 778 5 %RANDOM
Rwork0.15936 ---
all0.16128 14764 --
obs0.16128 14764 96.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.584 Å2
Baniso -1Baniso -2Baniso -3
1--0.78 Å20 Å20 Å2
2--0.18 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.85→42.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1494 0 75 181 1750
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221637
X-RAY DIFFRACTIONr_bond_other_d0.0010.021555
X-RAY DIFFRACTIONr_angle_refined_deg1.242.0262235
X-RAY DIFFRACTIONr_angle_other_deg0.69333605
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1645206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.83124.64356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.90415270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.635159
X-RAY DIFFRACTIONr_chiral_restr0.0750.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021796
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02293
X-RAY DIFFRACTIONr_nbd_refined0.1780.2236
X-RAY DIFFRACTIONr_nbd_other0.1730.21579
X-RAY DIFFRACTIONr_nbtor_refined0.1630.2754
X-RAY DIFFRACTIONr_nbtor_other0.0790.21004
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2141
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1990.2102
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1090.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4851.51085
X-RAY DIFFRACTIONr_mcbond_other0.1041.5422
X-RAY DIFFRACTIONr_mcangle_it0.70321650
X-RAY DIFFRACTIONr_scbond_it1.1213675
X-RAY DIFFRACTIONr_scangle_it1.7184.5585
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.199 51 -
Rwork0.196 814 -
obs--74.89 %
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)
14.2257-0.23810.27974.65570.47272.4431-0.0763-0.33850.06730.20360.0604-0.0035-0.0577-0.07560.0159-0.07170.0510.0125-0.0489-0.0093-0.19121.271325.92629.4044
25.8733-3.97280.65183.6203-0.03075.6377-0.077-0.0361-0.49850.25720.08610.35280.2784-0.1336-0.009-0.0899-0.01650.0436-0.16790.0372-0.080419.767417.899323.1634
33.80412.16020.80522.9635-0.44341.1681-0.05920.1365-0.0511-0.0166-0.0847-0.0421-0.1762-0.10080.1439-0.08740.0194-0.0134-0.11020.0115-0.107627.774328.515619.0805
46.62120.62462.2256.74170.34842.19050.058-0.0129-0.1466-0.21870.06430.0244-0.13970.0588-0.1222-0.11430.02010.0121-0.12760.0087-0.146912.841426.97118.7761
59.62352.0714-1.05329.2718-3.57952.4395-0.1089-0.1603-0.17430.4911-0.3407-1.1705-0.22550.18050.4496-0.1664-0.0255-0.1191-0.14580.07910.060539.235830.617223.8558
67.9017-4.41751.156711.9202-0.578717.45670.3376-0.0882-0.3741-0.30420.12021.1549-0.0442-1.3213-0.4578-0.1751-0.0212-0.0217-0.05370.0590.08251.904721.877918.4272
77.50070.47863.24842.71770.95145.00990.11570.13070.264-0.03330.1195-0.2255-0.17230.4307-0.2352-0.1436-0.02180.0138-0.06070.0581-0.085439.468531.369610.5594
810.4728-1.6846-0.022810.92261.87834.71460.23410.0255-0.0653-0.1632-0.14070.39050.1715-0.4212-0.0934-0.1433-0.0297-0.0156-0.08040.0965-0.14930.616634.853714.1932
915.1729-1.4774-1.10911.2237-1.83824.0796-0.00010.0758-0.1886-0.01230.06260.1106-0.0930.0913-0.0625-0.09680.01730.0114-0.12-0.001-0.126627.112930.99544.8867
1011.8604-1.2537-2.84253.0847-1.78512.15460.0474-0.1217-0.0439-0.0691-0.00960.04230.053-0.0894-0.0378-0.0896-0.00790.0063-0.1207-0.0039-0.133312.625839.367711.5583
113.86661.4967-2.7645.9896-2.6238.37020.08390.02490.23110.1618-0.02460.3631-0.4736-0.1093-0.0593-0.1094-0.0166-0.0296-0.11520.0278-0.085129.340933.068314.8901
125.1992-6.57545.22949.7835-5.79055.72150.42710.3579-0.096-0.3772-0.16220.360.42340.2248-0.2649-0.1006-0.0029-0.0125-0.08610.0064-0.090510.48729.434912.8734
132.554-2.41361.36552.5538-0.23824.78660.08660.0472-0.14580.0509-0.1131-0.1871-0.0622-0.03160.0265-0.0949-0.0040.0051-0.1050.0036-0.066529.023519.844519.6838
147.4513-2.4384-4.88072.7681-1.3487.6-0.3713-0.6087-0.16040.03020.51190.25360.13520.0426-0.1407-0.06260.03470.0178-0.02250.0172-0.091111.944228.804627.2285
152.0091-4.1032.20919.6384-9.007418.48340.24040.3193-0.6507-0.3959-0.45170.13170.18710.91240.2113-0.15870.03610.0545-0.04050.067-0.058539.033223.32910.501
168.29815.4636-7.372413.2674-7.010818.8040.1854-0.22480.58230.62660.17550.7241-0.3011-0.1882-0.3609-0.17880.06730.0155-0.11720.0584-0.04291.517636.543821.3718
1719.321-0.9969-14.90961.7669-1.286537.1123-0.0680.54871.05350.51090.1644-0.2135-0.1752-0.2901-0.0964-0.1679-0.0413-0.0858-0.18090.0234-0.029337.296524.418923.7698
1820.4645-14.1751.371720.07317.05657.2053-0.38710.493-0.12020.74240.2277-0.22310.37380.19870.1593-0.12970.04050.0909-0.05110.0409-0.05723.652823.508524.5337
193.1377-0.9554-0.97743.2662-0.09070.3552-0.05020.2354-0.173-0.1453-0.2844-0.30130.20760.30420.3347-0.1249-0.00290.0025-0.11690.0277-0.067935.918122.088217.4641
202.17911.8306-4.53965.9239-5.988310.53550.0163-0.34660.1169-0.18360.20630.590.03290.2697-0.2226-0.13090.0457-0.0127-0.05850.0472-0.05924.403929.731325.0699
216.6562-12.1211-6.35631.11387.185814.54420.3024-0.03240.4987-0.6061-0.0936-0.48-0.09950.1836-0.2087-0.16140.01760.0206-0.14770.0177-0.181919.671530.374714.0119
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 5
2X-RAY DIFFRACTION1A94 - 99
3X-RAY DIFFRACTION1A6 - 10
4X-RAY DIFFRACTION2B1 - 5
5X-RAY DIFFRACTION2B94 - 99
6X-RAY DIFFRACTION2B6 - 10
7X-RAY DIFFRACTION3A20 - 32
8X-RAY DIFFRACTION4B20 - 32
9X-RAY DIFFRACTION5A11 - 19
10X-RAY DIFFRACTION6B11 - 19
11X-RAY DIFFRACTION7A33 - 43
12X-RAY DIFFRACTION8B33 - 43
13X-RAY DIFFRACTION9A44 - 57
14X-RAY DIFFRACTION10B44 - 57
15X-RAY DIFFRACTION11A77 - 85
16X-RAY DIFFRACTION12B77 - 85
17X-RAY DIFFRACTION13A86 - 93
18X-RAY DIFFRACTION14B86 - 93
19X-RAY DIFFRACTION15A58 - 62
20X-RAY DIFFRACTION16B58 - 62
21X-RAY DIFFRACTION17A63 - 68
22X-RAY DIFFRACTION18B63 - 68
23X-RAY DIFFRACTION19A69 - 76
24X-RAY DIFFRACTION20B69 - 76
25X-RAY DIFFRACTION21A200

+
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