[English] 日本語
Yorodumi
- PDB-4mlf: Crystal structure for the complex of thrombin mutant D102N and hirudin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4mlf
TitleCrystal structure for the complex of thrombin mutant D102N and hirudin
Components
  • (Thrombin) x 2
  • Hirudin variant-1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Serine protease / ligand binding / hirudin / thrombin / conformational selection / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


negative regulation of serine-type peptidase activity / positive regulation of lipid kinase activity / cytolysis by host of symbiont cells / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / ligand-gated ion channel signaling pathway ...negative regulation of serine-type peptidase activity / positive regulation of lipid kinase activity / cytolysis by host of symbiont cells / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / negative regulation of astrocyte differentiation / negative regulation of platelet activation / positive regulation of collagen biosynthetic process / negative regulation of cytokine production involved in inflammatory response / positive regulation of blood coagulation / negative regulation of fibrinolysis / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / fibrinolysis / regulation of cytosolic calcium ion concentration / Intrinsic Pathway of Fibrin Clot Formation / Peptide ligand-binding receptors / positive regulation of release of sequestered calcium ion into cytosol / acute-phase response / Regulation of Complement cascade / negative regulation of proteolysis / Cell surface interactions at the vascular wall / lipopolysaccharide binding / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / serine-type endopeptidase inhibitor activity / positive regulation of insulin secretion / platelet activation / response to wounding / positive regulation of protein localization to nucleus / Golgi lumen / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of reactive oxygen species metabolic process / blood coagulation / antimicrobial humoral immune response mediated by antimicrobial peptide / Thrombin signalling through proteinase activated receptors (PARs) / heparin binding / regulation of cell shape / positive regulation of cell growth / G alpha (q) signalling events / collagen-containing extracellular matrix / blood microparticle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / serine-type endopeptidase activity / signaling receptor binding / positive regulation of cell population proliferation / calcium ion binding / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Thrombin Inhibitor (Hirudin); Chain I / Thrombin Inhibitor (Hirudin), subunit I / Hirudin / Proteinase inhibitor I14, hirudin / Thrombin inhibitor hirudin / Hirudin/antistatin / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / : ...Thrombin Inhibitor (Hirudin); Chain I / Thrombin Inhibitor (Hirudin), subunit I / Hirudin / Proteinase inhibitor I14, hirudin / Thrombin inhibitor hirudin / Hirudin/antistatin / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / : / Thrombin light chain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / Kringle-like fold / Distorted Sandwich / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Prothrombin / Hirudin variant-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Hirudo medicinalis (medicinal leech)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsVogt, A.D. / Pozzi, N. / Chen, Z. / Di Cera, E.
Citation
Journal: Biophys.Chem. / Year: 2014
Title: Essential role of conformational selection in ligand binding.
Authors: Vogt, A.D. / Pozzi, N. / Chen, Z. / Di Cera, E.
#1: Journal: J.Biol.Chem. / Year: 2004
Title: Molecular dissection of Na+ binding to thrombin.
Authors: Pineda, A.O. / Carrell, C.J. / Bush, L.A. / Prasad, S. / Caccia, S. / Chen, Z.W. / Mathews, F.S. / Di Cera, E.
History
DepositionSep 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Mar 5, 2014Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thrombin
B: Thrombin
D: Hirudin variant-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9658
Polymers40,5443
Non-polymers4215
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-30 kcal/mol
Surface area16330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.506, 89.506, 133.148
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

-
Protein , 2 types, 2 molecules BD

#2: Protein Thrombin


Mass: 29779.234 Da / Num. of mol.: 1 / Fragment: Thrombin heavy chain (UNP residues 364-622) / Mutation: D102N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Cell (production host): Kidney Fibroblast Cells (BHK-21) / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P00734, thrombin
#3: Protein Hirudin variant-1 / Hirudin-1 / Hirudin-I / Lepirudin


Mass: 6973.505 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hirudo medicinalis (medicinal leech) / Production host: Escherichia coli (E. coli) / References: UniProt: P01050

-
Protein/peptide / Sugars , 2 types, 2 molecules A

#1: Protein/peptide Thrombin


Mass: 3791.204 Da / Num. of mol.: 1 / Fragment: Thrombin light chain (UNP residues 331-363)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Cell (production host): Kidney Fibroblast Cells (BHK-21) / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P00734, thrombin
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 3 types, 102 molecules

#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 20% PEG 3350, 0.2M Ca acetate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 11, 2013
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→74.28 Å / Num. all: 28265 / Num. obs: 26993 / % possible obs: 95.5 % / Observed criterion σ(F): -0.5 / Observed criterion σ(I): -0.5 / Redundancy: 11.5 % / Biso Wilson estimate: 39.5 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 23.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
2.2-2.247.10.4813.313520.48197.6
2.24-2.287.50.4633.513220.46396.5
2.28-2.327.50.4353.713320.43596.2
2.32-2.377.70.414413370.41496.8
2.37-2.427.70.3814.313510.38196.2
2.42-2.4880.3694.713320.36996.8

-
Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPfrom ccp4phasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1SHH

1shh


Resolution: 2.2→40 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / SU B: 13.225 / SU ML: 0.145 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): -0.5 / σ(I): -0.5 / ESU R: 0.208 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2335 1348 5 %RANDOM
Rwork0.19818 ---
obs0.19996 25485 95.16 %-
all-26781 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.611 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å20 Å2
2---0.47 Å20 Å2
3---0.94 Å2
Refinement stepCycle: LAST / Resolution: 2.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2802 0 27 98 2927
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222905
X-RAY DIFFRACTIONr_angle_refined_deg1.4631.9673925
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7985350
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.18224.317139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.53115508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2061520
X-RAY DIFFRACTIONr_chiral_restr0.1050.2408
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212229
X-RAY DIFFRACTIONr_mcbond_it0.4871.51758
X-RAY DIFFRACTIONr_mcangle_it0.92322822
X-RAY DIFFRACTIONr_scbond_it1.77131147
X-RAY DIFFRACTIONr_scangle_it2.8774.51103
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 113 -
Rwork0.322 1861 -
obs-1861 96.72 %
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)
18.6794-2.167910.38462.9416-2.050912.8879-0.55460.40640.8085-0.2648-0.0236-0.2766-1.09380.38860.57820.4210.08960.31170.11490.12410.538411.41159.3156-17.7248
24.12911.25883.99145.8194-1.043110.04380.2568-0.1775-0.02480.52570.12760.56940.5523-1.3328-0.38440.1452-0.05320.04120.29580.00960.15995.07270.2189-7.7485
31.6161-0.72970.46615.0804-0.49992.84390.16780.2523-0.3373-0.1326-0.03880.03070.00840.012-0.12890.0660.0151-0.03140.0706-0.0750.091319.1667-7.3595-20.8459
46.634-0.65330.70643.51440.35142.81450.04850.2757-0.2114-0.45070.179-0.50270.13720.1194-0.22750.13480.00910.06610.071-0.05150.099928.3249-0.8894-20.7072
56.07981.17722.31443.26760.67523.30770.18020.2451-0.166-0.3382-0.0244-0.64160.21090.5305-0.15580.16910.09110.09520.2145-0.0540.175928.2642-7.4068-25.7849
64.1287-0.20860.8392.64350.0883.76670.1330.25990.1604-0.1333-0.0014-0.5159-0.10920.4586-0.13160.08690.0030.06490.0713-0.02670.190629.19032.9672-17.9719
71.3196-0.1929-0.03663.71872.88074.0267-0.0296-0.1890.04840.21580.0365-0.04370.0885-0.0127-0.00690.08990.03780.01170.0689-0.01020.027817.0338-2.6679-6.3977
80.0027-0.2186-0.191323.093716.238915.8258-0.03080.0093-0.011-0.0998-0.21791.1993-0.3207-0.62880.24870.23650.05420.03240.1876-0.03030.308420.9587-25.883-16.2078
93.98670.23110.96352.5244-0.23454.17240.1542-0.5339-0.09020.5632-0.0738-0.26820.23810.2657-0.08030.22770.0136-0.02460.1180.00640.087423.6826-8.1461-2.3914
102.71961.3308-0.56116.2731-1.46937.9989-0.0829-0.3207-0.30790.59810.15930.28160.81880.097-0.07630.25540.0680.01030.09720.01080.142519.0585-13.4931-5.239
111.961-0.8822-0.23424.0795-0.44451.72530.0047-0.2215-0.00770.37240.0815-0.16830.13740.0545-0.08610.10290.0055-0.02430.059-0.02070.030921.2827-1.9835-6.0958
129.93070.7205-12.97520.1331-14.495634.93790.47850.68571.3084-1.2624-0.2353-0.5454-1.34090.3222-0.24330.3946-0.1453-0.06160.26430.06350.574233.425212.6541-15.1334
136.73641.6260.19860.6908-0.92273.99390.085-0.1249-0.85810.057-0.1298-0.4080.3980.52280.04480.47370.214-0.27290.1604-0.07340.685235.4831-22.0906-5.952
1413.51172.1156-0.15456.56471.633410.9424-0.07770.2403-0.45060.3514-0.0095-0.66040.07670.5110.08720.35810.187-0.07230.3046-0.01140.668640.091-22.9621-6.5573
1520.320619.0214-9.324518.1143-6.289424.4879-0.6046-0.3246-1.8557-0.5465-0.2278-1.77170.35541.90210.83240.23670.32140.14070.67370.05170.478726.0952-10.349-35.5604
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 8
2X-RAY DIFFRACTION2A9 - 14
3X-RAY DIFFRACTION3B16 - 37
4X-RAY DIFFRACTION4B38 - 59
5X-RAY DIFFRACTION5B60 - 78
6X-RAY DIFFRACTION6B79 - 127
7X-RAY DIFFRACTION7B128 - 144
8X-RAY DIFFRACTION8B145 - 149
9X-RAY DIFFRACTION9B150 - 184
10X-RAY DIFFRACTION10B185 - 197
11X-RAY DIFFRACTION11B198 - 234
12X-RAY DIFFRACTION12B235 - 247
13X-RAY DIFFRACTION13D301 - 320
14X-RAY DIFFRACTION14D321 - 352
15X-RAY DIFFRACTION15D353 - 365

+
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