[English] 日本語
Yorodumi
- PDB-1tlp: CRYSTALLOGRAPHIC STRUCTURAL ANALYSIS OF PHOSPHORAMIDATES AS INHIB... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1tlp
TitleCRYSTALLOGRAPHIC STRUCTURAL ANALYSIS OF PHOSPHORAMIDATES AS INHIBITORS AND TRANSITION-STATE ANALOGS OF THERMOLYSIN
ComponentsTHERMOLYSIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / METALLOPROTEINASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


thermolysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Elastase; domain 1 - #10 / Elastase; domain 1 / PepSY domain / Peptidase propeptide and YPEB domain / : / Peptidase M4, C-terminal / FTP domain / Peptidase M4 domain / Peptidase M4 / Thermolysin metallopeptidase, catalytic domain ...Elastase; domain 1 - #10 / Elastase; domain 1 / PepSY domain / Peptidase propeptide and YPEB domain / : / Peptidase M4, C-terminal / FTP domain / Peptidase M4 domain / Peptidase M4 / Thermolysin metallopeptidase, catalytic domain / Thermolysin metallopeptidase, alpha-helical domain / Fungalysin/Thermolysin Propeptide Motif / Neutral Protease Domain 2 / Neutral Protease; domain 2 / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHORAMIDON / Chem-RDF / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsTronrud, D.E. / Monzingo, A.F. / Matthews, B.W.
Citation
Journal: Eur.J.Biochem. / Year: 1986
Title: Crystallographic structural analysis of phosphoramidates as inhibitors and transition-state analogs of thermolysin.
Authors: Tronrud, D.E. / Monzingo, A.F. / Matthews, B.W.
#1: Journal: Science / Year: 1987
Title: Structures of Two Thermolysin-Inhibitor Complexes that Differ by a Single Hydrogen Bond
Authors: Tronrud, D.E. / Holden, H.M. / Matthews, B.W.
#2: Journal: Biochemistry / Year: 1984
Title: An Interactive Computer Graphics Study of Thermolysin-Catalyzed Peptide Cleavage and Inhibition by N-Carboxymethyl Dipeptides
Authors: Hangauer, D.G. / Monzingo, A.F. / Matthews, B.W.
#3: Journal: Biochemistry / Year: 1984
Title: Binding of N-Carboxymethyl Dipepetide Inhibitors to Thermolysin Determined by X-Ray Crystallography. A Novel Class of Transition-State Analogues for Zinc Peptidases
Authors: Monzingo, A.F. / Matthews, B.W.
#4: Journal: Biochemistry / Year: 1983
Title: Structural Analysis of the Inhibition of Thermolysin by an Active-Site-Directed Irreversible Inhibitor
Authors: Holmes, M.A. / Tronrud, D.E. / Matthews, B.W.
#5: Journal: Biochemistry / Year: 1982
Title: Structure of a Mercaptan-Thermolysin Complex Illustrates Mode of Inhibition of Zinc Proteases by Substrate-Analogue Mercaptans
Authors: Monzingo, A.F. / Matthews, B.W.
#6: Journal: J.Mol.Biol. / Year: 1982
Title: Structure of Thermolysin Refined at 1.6 Angstroms Resolution
Authors: Holmes, M.A. / Matthews, B.W.
#7: Journal: Biochemistry / Year: 1981
Title: Binding of Hydroxamic Acid Inhibitors to Crystalline Thermolysin Suggests a Pentacoordinate Zinc Intermediate in Catalysis
Authors: Holmes, M.A. / Matthews, B.W.
#8: Journal: J.Biol.Chem. / Year: 1979
Title: Binding of the Biproduct Analog L-Benzylsuccinic Acid to Thermolysin Determined by X-Ray Crystallography
Authors: Bolognesi, M.C. / Matthews, B.W.
#9: Journal: J.Biol.Chem. / Year: 1977
Title: Comparison of the Structures of Carboxypeptidase a and Thermolysin
Authors: Kester, W.R. / Matthews, B.W.
#10: Journal: J.Mol.Biol. / Year: 1977
Title: A Crystallographic Study of the Complex of Phosphoramidon with Thermolysin. A Model for the Presumed Catalytic Transition State and for the Binding of Extended Substrates
Authors: Weaver, L.H. / Kester, W.R. / Matthews, B.W.
#11: Journal: Biochemistry / Year: 1977
Title: Crystallographic Study of the Binding of Dipeptide Inhibitors to Thermolysin. Implications for the Mechanism of Catalysis
Authors: Kester, W.R. / Matthews, B.W.
#12: Journal: Biochemistry / Year: 1976
Title: Role of Calcium in the Thermal Stability of Thermolysin
Authors: Dahlquist, F.W. / Long, J.W. / Bigbee, W.L.
#13: Journal: Proc.Natl.Acad.Sci.USA / Year: 1975
Title: Evidence of Homologous Relationship between Thermolysin and Neutral Protease a of Bacillus Subtilis
Authors: Levy, P.L. / Pangburn, M.K. / Burstein, Y. / Ericsson, L.H. / Neurath, H. / Walsh, K.A.
#14: Journal: Experientia,Suppl. / Year: 1976
Title: The Structure and Stability of Thermolysin
Authors: Weaver, L.H. / Kester, W.R. / Teneyck, L.F. / Matthews, B.W.
#15: Journal: J.Biol.Chem. / Year: 1974
Title: The Conformation of Thermolysin
Authors: Matthews, B.W. / Weaver, L.H. / Kester, W.R.
#16: Journal: Biochemistry / Year: 1974
Title: Binding of Lanthanide Ions to Thermolysin
Authors: Matthews, B.W. / Weaver, L.H.
#17: Journal: J.Mol.Biol. / Year: 1972
Title: The Structure of Thermolysin. An Electron Density Map at 2.3 Angstroms Resolution
Authors: Colman, P.M. / Jansonius, J.N. / Matthews, B.W.
#18: Journal: Nature New Biol. / Year: 1972
Title: Amino-Acid Sequence of Thermolysin
Authors: Titani, K. / Hermodson, M.A. / Ericsson, L.H. / Walsh, K.A. / Neurath, H.
#19: Journal: Nature New Biol. / Year: 1972
Title: Three Dimensional Structure of Thermolysin
Authors: Matthews, B.W. / Jansonius, J.N. / Colman, P.M. / Schoenborn, B.P. / Duporque, D.
#20: Journal: Nature New Biol. / Year: 1972
Title: Structure of Thermolysin
Authors: Matthews, B.W. / Colman, P.M. / Jansonius, J.N. / Titani, K. / Walsh, K.A. / Neurath, H.
#21: Journal: Macromolecules / Year: 1972
Title: The Gamma Turn. Evidence for a New Folded Conformation in Proteins
Authors: Matthews, B.W.
#22: Journal: Biochem.Biophys.Res.Commun. / Year: 1972
Title: Rare Earths as Isomorphous Calcium Replacements for Protein Crystallography
Authors: Colman, P.M. / Weaver, L.H. / Matthews, B.W.
History
DepositionJun 29, 1987Processing site: BNL
Revision 1.0Jan 9, 1989Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 2.0Nov 23, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / atom_sites ...atom_site / atom_sites / database_2 / database_PDB_matrix / pdbx_database_remark / pdbx_struct_conn_angle / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[1][2] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[2][2] / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][2] / _database_PDB_matrix.origx[2][1] / _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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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 / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Details: ORTHOGONAL X,Y,Z AXES WERE REALIGNED FROM A*,B,C TO A,B*,C CRYSTALLOGRAPHIC DIRECTIONS
Provider: repository / Type: Remediation
Revision 2.1Mar 13, 2024Group: Data collection / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond / pdbx_entity_src_syn
Remark 700SHEET THE *ACTIVE-SITE* SHEET SUBSTRUCTURE OF THIS MOLECULE HAS ONE EDGE-STRAND COMPRISED OF TWO ...SHEET THE *ACTIVE-SITE* SHEET SUBSTRUCTURE OF THIS MOLECULE HAS ONE EDGE-STRAND COMPRISED OF TWO DISTINCT SEQUENCES OF THE POLYPEPTIDE CHAIN. TO REPRESENT THIS FEATURE AN EXTRA SHEET IS DEFINED. STRANDS 2,3,4,5 OF S1 ARE IDENTICAL TO STRANDS 2,3,4,5 OF S2.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: THERMOLYSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1327
Polymers34,3621
Non-polymers7696
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.100, 94.100, 131.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Atom site foot note1: RESIDUE 51 IS A CIS-PROLINE. / 2: ATOMS 2601 - 2611 LIE IN SUBSITE S1. / 3: ATOMS 2619 - 2622 LIE IN SUBSITE S1(PRIME). / 4: ATOMS 2627 - 2636 LIE IN SUBSITE S2(PRIME). / 5: ATOM 2613 IS BONDED TO THE ZINC ATOM.

-
Components

#1: Protein THERMOLYSIN


Mass: 34362.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thermoproteolyticus (bacteria)
References: UniProt: P00800, thermolysin
#2: Chemical ChemComp-RDF / N-ALPHA-L-RHAMNOPYRANOSYLOXY(HYDROXYPHOSPHINYL)-L-LEUCYL-L-TRYPTOPHAN / PHOSPHORAMIDON


Type: peptide-like, Glycopeptide / Class: Enzyme inhibitor / Mass: 543.504 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H34N3O10P / References: PHOSPHORAMIDON
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.87 %
Crystal grow
*PLUS
pH: 7.2 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.01 Mcalcium acetate11
20.01 MTris acetate11
37 %(v/v)dimethylsulfoxide11

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.3→23.3 Å
Reflection
*PLUS

-
Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 2.3→23.3 Å /
RfactorNum. reflection
obs0.174 13523
Refinement stepCycle: LAST / Resolution: 2.3→23.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 42 163 2637
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.022
X-RAY DIFFRACTIONt_angle_deg2.9
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Refinement
*PLUS
Num. reflection obs: 13523
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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