[English] 日本語
Yorodumi
- PDB-4gtp: FTase in complex with BMS analogue 16 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4gtp
TitleFTase in complex with BMS analogue 16
Components
  • Protein farnesyltransferase subunit betaFarnesyltransferase
  • Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / protein prenylation / inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


Apoptotic cleavage of cellular proteins / Inactivation, recovery and regulation of the phototransduction cascade / RAS processing / protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein geranylgeranyltransferase type I / protein farnesylation / positive regulation of tubulin deacetylation / protein farnesyltransferase ...Apoptotic cleavage of cellular proteins / Inactivation, recovery and regulation of the phototransduction cascade / RAS processing / protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein geranylgeranyltransferase type I / protein farnesylation / positive regulation of tubulin deacetylation / protein farnesyltransferase / protein farnesyltransferase activity / protein farnesyltransferase complex / regulation of fibroblast proliferation / Rab geranylgeranyltransferase activity / protein geranylgeranylation / positive regulation of skeletal muscle acetylcholine-gated channel clustering / farnesyltranstransferase activity / negative regulation of nitric-oxide synthase biosynthetic process / microtubule associated complex / enzyme-linked receptor protein signaling pathway / positive regulation of nitric-oxide synthase biosynthetic process / positive regulation of Rac protein signal transduction / alpha-tubulin binding / response to inorganic substance / positive regulation of cell cycle / response to cytokine / wound healing / lipid metabolic process / response to organic cyclic compound / receptor tyrosine kinase binding / positive regulation of fibroblast proliferation / fibroblast proliferation / microtubule binding / cell population proliferation / molecular adaptor activity / negative regulation of cell population proliferation / positive regulation of cell population proliferation / negative regulation of apoptotic process / zinc ion binding / cytoplasm
Similarity search - Function
Protein farnesyltransferase subunit beta / Protein prenylyltransferase / Prenyltransferase subunit beta / Protein prenyltransferase, alpha subunit / Protein prenyltransferase alpha subunit repeat / Protein prenyltransferases alpha subunit repeat profile. / PFTB repeat / Prenyltransferase and squalene oxidase repeat / Glycosyltransferase - #20 / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid ...Protein farnesyltransferase subunit beta / Protein prenylyltransferase / Prenyltransferase subunit beta / Protein prenyltransferase, alpha subunit / Protein prenyltransferase alpha subunit repeat / Protein prenyltransferases alpha subunit repeat profile. / PFTB repeat / Prenyltransferase and squalene oxidase repeat / Glycosyltransferase - #20 / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Glycosyltransferase / Alpha/alpha barrel / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Chem-7TP / FARNESYL DIPHOSPHATE / Protein farnesyltransferase subunit beta / Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsGuo, Z. / Stigter, E.A. / Bon, R.S. / Waldmann, H. / Blankenfeldt, W. / Goody, R.S.
CitationJournal: J.Med.Chem. / Year: 2012
Title: Development of Selective, Potent RabGGTase Inhibitors
Authors: Stigter, E.A. / Guo, Z. / Bon, R.S. / Wu, Y.W. / Choidas, A. / Wolf, A. / Menninger, S. / Waldmann, H. / Blankenfeldt, W. / Goody, R.S.
History
DepositionAug 29, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
B: Protein farnesyltransferase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,2209
Polymers91,8472
Non-polymers1,3737
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9130 Å2
ΔGint-13 kcal/mol
Surface area28480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.650, 171.650, 70.005
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha / CAAX farnesyltransferase subunit alpha / FTase-alpha / Ras proteins prenyltransferase subunit alpha ...CAAX farnesyltransferase subunit alpha / FTase-alpha / Ras proteins prenyltransferase subunit alpha / Type I protein geranyl-geranyltransferase subunit alpha / GGTase-I-alpha


Mass: 44098.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Fnta / Plasmid: pGATEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CODON-PLUS RIL (DE3)
References: UniProt: Q04631, protein farnesyltransferase, protein geranylgeranyltransferase type I
#2: Protein Protein farnesyltransferase subunit beta / Farnesyltransferase / FTase-beta / CAAX farnesyltransferase subunit beta / Ras proteins prenyltransferase subunit beta


Mass: 47749.340 Da / Num. of mol.: 1 / Fragment: C-terminal 10 residues deleted
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Fntb / Plasmid: pET27b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CODON-PLUS RIL (DE3) / References: UniProt: Q02293, protein farnesyltransferase

-
Non-polymers , 5 types, 135 molecules

#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-FPP / FARNESYL DIPHOSPHATE / Farnesyl pyrophosphate


Mass: 382.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H28O7P2
#6: Chemical ChemComp-7TP / 5-{(3R)-3-(4-hydroxybenzyl)-4-[(4-methoxyphenyl)sulfonyl]-1-[(1-methyl-1H-imidazol-5-yl)methyl]-2,3,4,5-tetrahydro-1H-1,4-benzodiazepin-7-yl}furan-2-carbaldehyde


Mass: 612.695 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H32N4O6S
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 3.24 Å3/Da / Density % sol: 62.05 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% (w/v) PEG 4000, 0.2M MgCl2, 0.1M Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→29.91 Å / Num. all: 30875 / Num. obs: 30855 / % possible obs: 99.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 47.8 Å2 / Rsym value: 0.078 / Net I/σ(I): 17.8
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 5 / Rsym value: 0.36 / % possible all: 100

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
PHASESphasing
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EU5

3eu5


Resolution: 2.75→29.91 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.919 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 23.052 / SU ML: 0.204 / Cross valid method: THROUGHOUT / ESU R: 0.554 / ESU R Free: 0.288 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22565 1557 5 %RANDOM
Rwork0.17671 ---
obs0.17922 29277 99.97 %-
all-30875 --
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 max: 140.5 Å2 / Biso mean: 42.888 Å2 / Biso min: 16.54 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20.18 Å20 Å2
2--0.35 Å20 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 2.75→29.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5853 0 85 128 6066
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0226097
X-RAY DIFFRACTIONr_bond_other_d00.024132
X-RAY DIFFRACTIONr_angle_refined_deg1.8831.9628281
X-RAY DIFFRACTIONr_angle_other_deg4.0383.0019969
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0865718
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.68923.987311
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.313151016
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3361542
X-RAY DIFFRACTIONr_chiral_restr0.1080.2878
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026770
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021253
X-RAY DIFFRACTIONr_nbd_refined0.2640.21928
X-RAY DIFFRACTIONr_nbd_other0.2550.24558
X-RAY DIFFRACTIONr_nbtor_refined0.2080.23029
X-RAY DIFFRACTIONr_nbtor_other0.1110.23004
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2265
X-RAY DIFFRACTIONr_metal_ion_refined0.0760.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.310.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2980.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.29
X-RAY DIFFRACTIONr_mcbond_it0.8171.53590
X-RAY DIFFRACTIONr_mcbond_other01.51441
X-RAY DIFFRACTIONr_mcangle_it1.52425795
X-RAY DIFFRACTIONr_scbond_it2.13132507
X-RAY DIFFRACTIONr_scangle_it3.344.52485
LS refinement shellResolution: 2.75→2.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 107 -
Rwork0.272 2154 -
obs--100 %
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)
10.4677-0.614-0.12641.0940.36070.4793-0.0251-0.0343-0.03930.0075-0.01210.11390.1211-0.00350.03720.01070.06720.0461-0.06830.0263-0.021754.087438.02442.6588
20.39890.0034-0.13140.72960.11090.8820.02330.05030.0541-0.0895-0.0635-0.06790.03040.1180.0402-0.06970.07440.03650.01110.0661-0.025462.264650.5315-9.3533
322.5221-6.90210.82582.6814-2.14267.64190.2949-2.1251-0.9858-1.835-0.50040.6657-0.5466-0.18020.2055-0.00310.002-0.0019-0.00080.0010.001951.849150.2218-0.3562
40000000000000000.0012-0.0011-0.00280.0007-0.00120.00252.544847.4125-9.7882
534.11755.5681-10.00383.8253-3.6684.35370.4133-0.55270.557-0.1785-0.67310.53150.12290.14830.2598-0.0020.0043-0.0019-0.0003-0.0009-0.002756.007945.2708-2.324
61.1163-0.2902-6.98480.07551.81643.70560.04250.5580.60990.9362-0.20230.3329-0.8088-0.05070.15980.00050.00060.0035-0.00040.0009-0.001951.483751.6619-4.1882
70.2356-0.1345-0.10580.58850.27250.4949-0.02150.0093-0.0184-0.03560.03020.06940.01770.023-0.0086-0.04610.07980.03350.00210.0601-0.015655.57646.2512-5.4874
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A55 - 369
2X-RAY DIFFRACTION2B21 - 423
3X-RAY DIFFRACTION3A401
4X-RAY DIFFRACTION3B504 - 506
5X-RAY DIFFRACTION4B501
6X-RAY DIFFRACTION5B502
7X-RAY DIFFRACTION6B503
8X-RAY DIFFRACTION7A501 - 557
9X-RAY DIFFRACTION7B601 - 671

+
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