[English] 日本語
Yorodumi
- PDB-5ac1: Sheep aldehyde dehydrogenase 1A1 with duocarmycin analog inhibitor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ac1
TitleSheep aldehyde dehydrogenase 1A1 with duocarmycin analog inhibitor
ComponentsRETINAL DEHYDROGENASE 1
KeywordsOXIDOREDUCTASE / OXIDATION-REDUCTION PROCESS / ALDEHYDE DEHYDROGENASE ACTIVITY
Function / homology
Function and homology information


fructosamine catabolic process / 3-deoxyglucosone dehydrogenase activity / benzaldehyde dehydrogenase (NAD+) / acetaldehyde dehydrogenase (NAD+) activity / benzaldehyde dehydrogenase (NAD+) activity / aminobutyraldehyde dehydrogenase / retinal dehydrogenase / gamma-aminobutyric acid biosynthetic process / aminobutyraldehyde dehydrogenase (NAD+) activity / maintenance of lens transparency ...fructosamine catabolic process / 3-deoxyglucosone dehydrogenase activity / benzaldehyde dehydrogenase (NAD+) / acetaldehyde dehydrogenase (NAD+) activity / benzaldehyde dehydrogenase (NAD+) activity / aminobutyraldehyde dehydrogenase / retinal dehydrogenase / gamma-aminobutyric acid biosynthetic process / aminobutyraldehyde dehydrogenase (NAD+) activity / maintenance of lens transparency / aldehyde dehydrogenase (NAD+) / cellular detoxification of aldehyde / aldehyde dehydrogenase (NAD+) activity / retinal dehydrogenase (NAD+) activity / retinol metabolic process / retinoid metabolic process / NAD binding / axon / synapse / cytosol
Similarity search - Function
Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family ...Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-K9P / Chem-TXE / Aldehyde dehydrogenase 1A1
Similarity search - Component
Biological speciesOVIS ARIES (sheep)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsKoch, M.F. / Harteis, S. / Blank, I.D. / Pestel, G. / Tietze, L.F. / Ochsenfeld, C. / Schneider, S. / Sieber, S.A.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: Structural, Biochemical, and Computational Studies Reveal the Mechanism of Selective Aldehyde Dehydrogenase 1A1 Inhibition by Cytotoxic Duocarmycin Analogues.
Authors: Koch, M.F. / Harteis, S. / Blank, I.D. / Pestel, G. / Tietze, L.F. / Ochsenfeld, C. / Schneider, S. / Sieber, S.A.
History
DepositionAug 11, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Database references
Revision 1.2Nov 18, 2015Group: Database references
Revision 1.3Jun 20, 2018Group: Advisory / Data collection / Derived calculations
Category: database_PDB_caveat / pdbx_struct_conn_angle ...database_PDB_caveat / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn
Item: _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._pdbx_struct_conn_angle.ptnr1_auth_asym_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.ptnr3_auth_asym_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.value
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RETINAL DEHYDROGENASE 1
B: RETINAL DEHYDROGENASE 1
C: RETINAL DEHYDROGENASE 1
D: RETINAL DEHYDROGENASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,49916
Polymers219,5424
Non-polymers3,95712
Water13,025723
1
A: RETINAL DEHYDROGENASE 1
B: RETINAL DEHYDROGENASE 1
hetero molecules

A: RETINAL DEHYDROGENASE 1
B: RETINAL DEHYDROGENASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,49916
Polymers219,5424
Non-polymers3,95712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area21340 Å2
ΔGint-107.3 kcal/mol
Surface area57630 Å2
MethodPISA
2
C: RETINAL DEHYDROGENASE 1
D: RETINAL DEHYDROGENASE 1
hetero molecules

C: RETINAL DEHYDROGENASE 1
D: RETINAL DEHYDROGENASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,49916
Polymers219,5424
Non-polymers3,95712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y,-z+21
Buried area20720 Å2
ΔGint-105.9 kcal/mol
Surface area58240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)188.336, 80.953, 172.331
Angle α, β, γ (deg.)90.00, 118.13, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2031-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 7 - 500 / Label seq-ID: 8 - 501

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

NCS oper: (Code: given
Matrix: (0.8249, -0.000346, 0.5653), (-0.00016, -1, -0.00038), (0.5653, 0.000223, -0.8249)
Vector: -33.56, 95.43, 108.3)

-
Components

#1: Protein
RETINAL DEHYDROGENASE 1 / RALDH 1 / RALDH1 / ALDH-E1 / ALHDII / ALDEHYDE DEHYDROGENASE FAMILY 1 MEMBER A1 / ALDEHYDE ...RALDH 1 / RALDH1 / ALDH-E1 / ALHDII / ALDEHYDE DEHYDROGENASE FAMILY 1 MEMBER A1 / ALDEHYDE DEHYDROGENASE CYTOSOLIC / ALDEHYDE DEHYDROGENASE 1A1


Mass: 54885.590 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) OVIS ARIES (sheep) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P51977, retinal dehydrogenase
#2: Chemical
ChemComp-K9P / 1-[(1S)-1-methyl-5-oxidanyl-1,2-dihydrobenzo[e]indol-3-yl]hexan-1-one


Mass: 297.391 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H23NO2
#3: Chemical
ChemComp-TXE / [[(2R,3S,4R,5R)-5-[(3R)-3-aminocarbonyl-3,4-dihydro-2H-pyridin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanidyl-ph osphoryl] [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphate / 1,2,3,4-TETRAHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE


Mass: 667.457 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H31N7O14P2
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 723 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 26.2 % / Description: NONE
Crystal growTemperature: 277 K
Details: 100 MM BIS-TRIS, PH 6.0, 4.5-7% PEG5000, 150=225MM MGCL2, 4DEGREE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→49.4 Å / Num. obs: 134836 / % possible obs: 98.4 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 8.9
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 1.7 / % possible all: 84.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4X4L

4x4l


Resolution: 2.08→49.38 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.899 / SU B: 6.556 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.25 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26494 6743 5 %RANDOM
Rwork0.22872 ---
obs0.23052 128092 98.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.807 Å2
Baniso -1Baniso -2Baniso -3
1-1.27 Å20 Å20.05 Å2
2---0.36 Å20 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 2.08→49.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15225 0 268 723 16216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01916077
X-RAY DIFFRACTIONr_bond_other_d0.0070.0215217
X-RAY DIFFRACTIONr_angle_refined_deg1.6371.97321808
X-RAY DIFFRACTIONr_angle_other_deg1.203335186
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.38952026
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.28624.735678
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.501152730
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3931570
X-RAY DIFFRACTIONr_chiral_restr0.0940.22360
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02118549
X-RAY DIFFRACTIONr_gen_planes_other0.0060.023615
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0042.6318002
X-RAY DIFFRACTIONr_mcbond_other2.0042.6318003
X-RAY DIFFRACTIONr_mcangle_it2.8253.94210033
X-RAY DIFFRACTIONr_mcangle_other2.8253.94110033
X-RAY DIFFRACTIONr_scbond_it2.5432.928075
X-RAY DIFFRACTIONr_scbond_other2.5432.928076
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7834.27911765
X-RAY DIFFRACTIONr_long_range_B_refined5.09221.518599
X-RAY DIFFRACTIONr_long_range_B_other5.05321.46218382
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A307680.06
12B307680.06
21A307740.07
22C307740.07
31A307150.06
32D307150.06
41B310200.07
42C310200.07
51B307730.06
52D307730.06
61C304730.07
62D304730.07
LS refinement shellResolution: 2.082→2.136 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.458 404 -
Rwork0.442 7657 -
obs--79.69 %

+
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