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Basic information

Entry
Database: PDB / ID: 1dva
TitleCrystal Structure of the Complex Between the Peptide Exosite Inhibitor E-76 and Coagulation Factor VIIA
Components
  • (DES-GLA FACTOR VIIA ...) x 2
  • PEPTIDE E-76
KeywordsHYDROLASE/HYDROLASE INHIBITOR / protein-peptide complex / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


coagulation factor VIIa / response to Thyroid stimulating hormone / response to 2,3,7,8-tetrachlorodibenzodioxine / response to astaxanthin / response to thyrotropin-releasing hormone / response to genistein / serine-type peptidase complex / positive regulation of platelet-derived growth factor receptor signaling pathway / response to vitamin K / response to carbon dioxide ...coagulation factor VIIa / response to Thyroid stimulating hormone / response to 2,3,7,8-tetrachlorodibenzodioxine / response to astaxanthin / response to thyrotropin-releasing hormone / response to genistein / serine-type peptidase complex / positive regulation of platelet-derived growth factor receptor signaling pathway / response to vitamin K / response to carbon dioxide / response to thyroxine / positive regulation of leukocyte chemotaxis / response to cholesterol / response to growth hormone / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of TOR signaling / positive regulation of blood coagulation / animal organ regeneration / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Removal of aminoterminal propeptides from gamma-carboxylated proteins / serine-type peptidase activity / BMAL1:CLOCK,NPAS2 activates circadian gene expression / protein processing / Golgi lumen / circadian rhythm / response to estrogen / blood coagulation / response to estradiol / collagen-containing extracellular matrix / vesicle / response to hypoxia / positive regulation of cell migration / endoplasmic reticulum lumen / signaling receptor binding / serine-type endopeptidase activity / calcium ion binding / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Peptidase S1A, coagulation factor VII/IX/X/C/Z / Coagulation factor-like, Gla domain superfamily / Coagulation Factor Xa inhibitory site / Laminin / Laminin / EGF-type aspartate/asparagine hydroxylation site / EGF-like domain / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. ...Peptidase S1A, coagulation factor VII/IX/X/C/Z / Coagulation factor-like, Gla domain superfamily / Coagulation Factor Xa inhibitory site / Laminin / Laminin / EGF-type aspartate/asparagine hydroxylation site / EGF-like domain / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like 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. / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Ribbon / 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 domain profile. / Serine proteases, trypsin family, serine active site. / 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
D-Phe-Phe-Arg Chloromethylketone / beta-lactose / Chem-0Z6 / CACODYLATE ION / alpha-L-fucopyranose / beta-L-fucopyranose / alpha-D-glucopyranose / Coagulation factor VII
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsEigenbrot, C. / Ultsch, M.H.
CitationJournal: Nature / Year: 2000
Title: Peptide exosite inhibitors of factor VIIa as anticoagulants.
Authors: Dennis, M.S. / Eigenbrot, C. / Skelton, N.J. / Ultsch, M.H. / Santell, L. / Dwyer, M.A. / O'Connell, M.P. / Lazarus, R.A.
History
DepositionJan 20, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2000Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: DES-GLA FACTOR VIIA (HEAVY CHAIN)
L: DES-GLA FACTOR VIIA (LIGHT CHAIN)
X: PEPTIDE E-76
I: DES-GLA FACTOR VIIA (HEAVY CHAIN)
M: DES-GLA FACTOR VIIA (LIGHT CHAIN)
Y: PEPTIDE E-76
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,04919
Polymers82,5926
Non-polymers2,45713
Water724
1
H: DES-GLA FACTOR VIIA (HEAVY CHAIN)
L: DES-GLA FACTOR VIIA (LIGHT CHAIN)
X: PEPTIDE E-76
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,68810
Polymers41,2963
Non-polymers1,3927
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-14 kcal/mol
Surface area18150 Å2
MethodPISA
2
I: DES-GLA FACTOR VIIA (HEAVY CHAIN)
M: DES-GLA FACTOR VIIA (LIGHT CHAIN)
Y: PEPTIDE E-76
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3619
Polymers41,2963
Non-polymers1,0666
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-15 kcal/mol
Surface area18250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.490, 55.260, 111.730
Angle α, β, γ (deg.)90.00, 99.48, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
77
88
99
1010
/ NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

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Components

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DES-GLA FACTOR VIIA ... , 2 types, 4 molecules HILM

#1: Protein DES-GLA FACTOR VIIA (HEAVY CHAIN)


Mass: 28103.256 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: LIVER / Plasmid: PCMV5 / Cell line (production host): HUMAN KIDNEY CELL LINE 293 / Production host: Homo sapiens (human) / References: UniProt: P08709, coagulation factor VIIa
#2: Protein DES-GLA FACTOR VIIA (LIGHT CHAIN)


Mass: 10994.179 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: LIVER / Plasmid: PCMV5 / Cell line (production host): HUMAN KIDNEY CELL LINE 293 / Production host: Homo sapiens (human) / References: UniProt: P08709, coagulation factor VIIa

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Protein/peptide , 1 types, 2 molecules XY

#3: Protein/peptide PEPTIDE E-76


Mass: 2198.461 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Peptide E-76 was synthesized on a solid support, then cleaved and purified

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Sugars , 4 types, 5 molecules

#4: Polysaccharide beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(3+1)][b-D-Glcp]{[(4+1)][b-D-Galp]{}}}LINUCSPDB-CARE
#8: Sugar ChemComp-FUC / alpha-L-fucopyranose / Fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#9: Sugar ChemComp-GLC / alpha-D-glucopyranose / Glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#10: Sugar ChemComp-FUL / beta-L-fucopyranose / 6-DEOXY-BETA-L-GALACTOSE / Fucose


Type: L-saccharide, beta linking / Mass: 164.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-fucopyranoseCOMMON NAMEGMML 1.0
b-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 12 molecules

#5: Chemical ChemComp-0Z6 / D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-phenylalaninamide / FFRCK


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 504.045 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H36ClN6O3 / References: D-Phe-Phe-Arg Chloromethylketone
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsTHE INHIBITOR IS BOUND TO THE ACTIVE SITE OF THE ENZYME. THE UNBOUND FORM OF THE INHIBITOR IS D-PHE- ...THE INHIBITOR IS BOUND TO THE ACTIVE SITE OF THE ENZYME. THE UNBOUND FORM OF THE INHIBITOR IS D-PHE-PHE-ARG-CHLOROMETHYLKETONE. UPON REACTION WITH PROTEIN IT FORMS TWO COVALENT BONDS: 1) A COVALENT BOND TO SER 195 FORMING A HEMIKETAL AR7 AND 2) A COVALENT BOND TO NE2 OF HIS 57

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.18 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: PEG4000, t-butanol, sodium cacodylate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 %(w/v)PEG40001reservoir
210 %t-butanol1reservoir
30.1 Msodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 9, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 16915 / Num. obs: 16915 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 56 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 6.2
Reflection shellResolution: 3→3.16 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.262 / Mean I/σ(I) obs: 2.7 / Num. unique all: 2478 / % possible all: 98.4
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 99 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
TRUNCATEdata reduction
AMoREphasing
X-PLOR3.851refinement
CCP4(TRUNCATE)data scaling
RefinementResolution: 3→50 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0.2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: BULK SOLVENT MODEL WAS APPLIED THERE IS UNPUBLISHED EXPERIMENTAL EVIDENCE THAT THE CARBOHYDRATE ATTACHED TO CHAINS L AND M DIFFERS FROM THAT DESCRIBED IN THIS ENTRY. SER 52 CARRIES 2 OR 3 ...Details: BULK SOLVENT MODEL WAS APPLIED THERE IS UNPUBLISHED EXPERIMENTAL EVIDENCE THAT THE CARBOHYDRATE ATTACHED TO CHAINS L AND M DIFFERS FROM THAT DESCRIBED IN THIS ENTRY. SER 52 CARRIES 2 OR 3 GLUCOSE RESIDUES, AND SER 60 CARRIES ALPHA-L-FUCOSE. THE ELECTRON DENSITY IN THIS REGION IS IMPERFECT, AND WAS FIT WITHOUT THIS INFORMATION. THE FIT IS ONLY MODERATELY SUCCESFUL.
RfactorNum. reflection% reflectionSelection details
Rfree0.295 654 3.9 %RANDOM
Rwork0.225 ---
all0.228 16915 --
obs0.228 16915 97.5 %-
Displacement parametersBiso mean: 49.2 Å2
Baniso -1Baniso -2Baniso -3
1-3.62 Å20 Å23.49 Å2
2---4.9 Å20 Å2
3---1.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.68 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5768 0 145 4 5917
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_deg2
X-RAY DIFFRACTIONx_dihedral_angle_d26.3
X-RAY DIFFRACTIONx_improper_angle_d0.8
X-RAY DIFFRACTIONx_mcbond_it3.34
X-RAY DIFFRACTIONx_mcangle_it5.34
X-RAY DIFFRACTIONx_scbond_it3.24
X-RAY DIFFRACTIONx_scangle_it4.54
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Weight Biso : 1 / Weight position: 200

Ens-IDDom-IDNCS model detailsRms dev Biso (Å2)Rms dev position (Å)
11RESTRAIN0.380.045
220.320.042
330.420.053
440.340.033
550.380.041
661.030.055
770.950.147
881.030.062
991.230.044
10100.840.055
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.361 93 3.3 %
Rwork0.35 2745 -
obs--98.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM3MOD.CHOTMPTOPCHO.CHO
X-RAY DIFFRACTION3PARAM_CHO.LINKTOP.CAC
X-RAY DIFFRACTION4PARAM.CACTOP.DPN
X-RAY DIFFRACTION5PARAM.DPNTOP.CALCIUM
X-RAY DIFFRACTION6PARAM.CALCIUMTOP.CH2
X-RAY DIFFRACTION7PARWAT.PROTOP.LINK
X-RAY DIFFRACTION8PARAM.CH2TOPWAT.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 0.2 / % reflection Rfree: 3.9 % / Rfactor obs: 0.225
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 49.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg2
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.8
X-RAY DIFFRACTIONx_mcbond_it3.34
X-RAY DIFFRACTIONx_scbond_it3.24
X-RAY DIFFRACTIONx_mcangle_it5.34
X-RAY DIFFRACTIONx_scangle_it4.54
LS refinement shell
*PLUS
Rfactor Rfree: 0.361 / % reflection Rfree: 3.3 % / Rfactor Rwork: 0.35

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