[English] 日本語
Yorodumi
- PDB-4w93: Human pancreatic alpha-amylase in complex with montbretin A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4w93
TitleHuman pancreatic alpha-amylase in complex with montbretin A
ComponentsPancreatic alpha-amylase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Amylase / Glucosyl Hydrolase / Enzyme Inhibitor / Diabetes / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


polysaccharide digestion / Digestion of dietary carbohydrate / alpha-amylase / carbohydrate catabolic process / alpha-amylase activity / chloride ion binding / carbohydrate metabolic process / calcium ion binding / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Alpha-amylase, C-terminal domain / Aamy_C / Alpha-amylase/branching enzyme, C-terminal all beta / Alpha amylase, C-terminal all-beta domain / Alpha amylase / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta ...Alpha-amylase, C-terminal domain / Aamy_C / Alpha-amylase/branching enzyme, C-terminal all beta / Alpha amylase, C-terminal all-beta domain / Alpha amylase / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Montbretin A / Pancreatic alpha-amylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.352 Å
AuthorsWilliams, L.K. / Caner, S. / Brayer, G.D.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Nat.Chem.Biol. / Year: 2015
Title: The amylase inhibitor montbretin A reveals a new glycosidase inhibition motif.
Authors: Williams, L.K. / Zhang, X. / Caner, S. / Tysoe, C. / Nguyen, N.T. / Wicki, J. / Williams, D.E. / Coleman, J. / McNeill, J.H. / Yuen, V. / Andersen, R.J. / Withers, S.G. / Brayer, G.D.
History
DepositionAug 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Database references
Revision 1.2Sep 2, 2015Group: Database references
Revision 1.3Aug 23, 2017Group: Data collection / Derived calculations / Refinement description
Category: diffrn_detector / pdbx_struct_oper_list / software
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation / _software.version
Revision 1.4Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Dec 25, 2019Group: Database references / Polymer sequence / Category: entity_poly / struct_ref_seq_dif / Item: _entity_poly.pdbx_seq_one_letter_code_can
Revision 2.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pancreatic alpha-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2364
Polymers55,9311
Non-polymers1,3053
Water8,431468
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.370, 74.100, 135.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Pancreatic alpha-amylase / PA / 1 / 4-alpha-D-glucan glucanohydrolase


Mass: 55931.305 Da / Num. of mol.: 1 / Fragment: UNP residues 16-511
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AMY2A / Organ: Pancreas / Production host: Komagataella pastoris (fungus) / References: UniProt: P04746, alpha-amylase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-3L9 / Montbretin A / 2-(4-{[4-O-(6-deoxy-alpha-L-mannopyranosyl)-beta-D-xylopyranosyl]oxy}-3,5-dihydroxyphenyl)-5,7-dihydroxy-4-oxo-4H-chromen-3-yl beta-D-glucopyranosyl-(1->2)-6-O-[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]-beta-D-glucopyranosyl-(1->2)-6-deoxy-alpha-L-mannopyranoside


Mass: 1229.055 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C53H64O33
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 468 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.81 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 58% MPD, 100 mM sodium cacodylate

-
Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.283574 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.283574 Å / Relative weight: 1
ReflectionResolution: 1.352→37.05 Å / Num. obs: 42888 / % possible obs: 99 % / Redundancy: 6.3 % / Biso Wilson estimate: 14.82 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.062 / Net I/σ(I): 16.67
Reflection shellResolution: 1.35→1.39 Å / Redundancy: 3.66 % / Rmerge(I) obs: 0.887 / Mean I/σ(I) obs: 1.47 / % possible all: 88.9

-
Processing

SoftwareName: PHENIX / Version: 1.9_1683 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.352→37.05 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / Phase error: 22.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2113 5752 5 %Random
Rwork0.1976 ---
obs0.1983 115012 99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.5 Å2
Refinement stepCycle: LAST / Resolution: 1.352→37.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3945 0 88 468 4501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124159
X-RAY DIFFRACTIONf_angle_d1.2925657
X-RAY DIFFRACTIONf_dihedral_angle_d13.2121461
X-RAY DIFFRACTIONf_chiral_restr0.142583
X-RAY DIFFRACTIONf_plane_restr0.007733
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3521-1.36740.40761520.38662878X-RAY DIFFRACTION80
1.3674-1.38350.3751850.35353513X-RAY DIFFRACTION96
1.3835-1.40040.32171880.31743568X-RAY DIFFRACTION99
1.4004-1.41810.32141920.28943645X-RAY DIFFRACTION100
1.4181-1.43680.30021900.27893609X-RAY DIFFRACTION100
1.4368-1.45650.29081920.28133652X-RAY DIFFRACTION100
1.4565-1.47730.25751900.26693616X-RAY DIFFRACTION100
1.4773-1.49930.25181930.2553660X-RAY DIFFRACTION100
1.4993-1.52280.27371900.25373614X-RAY DIFFRACTION100
1.5228-1.54770.26881930.24943664X-RAY DIFFRACTION100
1.5477-1.57440.23281920.22563642X-RAY DIFFRACTION100
1.5744-1.6030.24811900.22143623X-RAY DIFFRACTION100
1.603-1.63390.22951940.22363671X-RAY DIFFRACTION100
1.6339-1.66720.26331910.21833632X-RAY DIFFRACTION100
1.6672-1.70350.22881930.21373674X-RAY DIFFRACTION100
1.7035-1.74310.22261920.21343652X-RAY DIFFRACTION100
1.7431-1.78670.21771920.2073629X-RAY DIFFRACTION100
1.7867-1.8350.21631930.20513675X-RAY DIFFRACTION100
1.835-1.8890.25791950.20763707X-RAY DIFFRACTION100
1.889-1.950.2471910.2143635X-RAY DIFFRACTION99
1.95-2.01970.21151940.20043675X-RAY DIFFRACTION100
2.0197-2.10050.22291920.20223656X-RAY DIFFRACTION100
2.1005-2.19610.18681920.19623654X-RAY DIFFRACTION100
2.1961-2.31190.2171940.20053680X-RAY DIFFRACTION99
2.3119-2.45670.19481950.19273696X-RAY DIFFRACTION100
2.4567-2.64630.2181940.18613697X-RAY DIFFRACTION100
2.6463-2.91250.21951970.18783743X-RAY DIFFRACTION100
2.9125-3.33370.18461970.18053739X-RAY DIFFRACTION100
3.3337-4.19920.16961990.15273787X-RAY DIFFRACTION100
4.1992-37.06390.16062100.16453974X-RAY DIFFRACTION100

+
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