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- PDB-6zov: ENTEROPEPTIDASE IN COMPLEX WITH COMPOUND 6 -

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Basic information

Entry
Database: PDB / ID: 6zov
TitleENTEROPEPTIDASE IN COMPLEX WITH COMPOUND 6
ComponentsEnteropeptidase
KeywordsHYDROLASE / PEPTIDASE
Function / homology
Function and homology information


enteropeptidase / brush border / serine-type endopeptidase activity / proteolysis / membrane
Similarity search - Function
Peptidase S1A, enteropeptidase / Scavenger receptor cysteine-rich domain / Domain found in sea urchin sperm protein, enterokinase, agrin / SRCR domain / SRCR domain profile. / SRCR-like domain / SRCR-like domain superfamily / Scavenger receptor Cys-rich / MAM domain signature. / SEA domain superfamily ...Peptidase S1A, enteropeptidase / Scavenger receptor cysteine-rich domain / Domain found in sea urchin sperm protein, enterokinase, agrin / SRCR domain / SRCR domain profile. / SRCR-like domain / SRCR-like domain superfamily / Scavenger receptor Cys-rich / MAM domain signature. / SEA domain superfamily / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / SEA domain profile. / SEA domain / SEA domain / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / 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 / Concanavalin A-like lectin/glucanase domain superfamily / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
4-carbamimidamidobenzoic acid / TRIETHYLENE GLYCOL / Enteropeptidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.19 Å
AuthorsCummings, M.D.
CitationJournal: J.Pharmacol.Exp.Ther. / Year: 2020
Title: Targeting Enteropeptidase with Reversible Covalent Inhibitors To Achieve Metabolic Benefits.
Authors: Sun, W. / Zhang, X. / Cummings, M.D. / Albarazanji, K. / Wu, J. / Wang, M. / Alexander, R. / Zhu, B. / Zhang, Y. / Leonard, J. / Lanter, J. / Lenhard, J.
History
DepositionJul 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Enteropeptidase
B: Enteropeptidase
C: Enteropeptidase
D: Enteropeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,85016
Polymers105,5194
Non-polymers1,33112
Water8,125451
1
A: Enteropeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7093
Polymers26,3801
Non-polymers3292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Enteropeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8076
Polymers26,3801
Non-polymers4275
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Enteropeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5592
Polymers26,3801
Non-polymers1791
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Enteropeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7755
Polymers26,3801
Non-polymers3954
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.925, 147.517, 147.518
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 233
2010B1 - 233
1020A1 - 234
2020C1 - 234
1030A1 - 233
2030D1 - 233
1040B1 - 233
2040C1 - 233
1050B1 - 235
2050D1 - 235
1060C1 - 233
2060D1 - 233

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Enteropeptidase / / Enterokinase / Serine protease 7 / Transmembrane protease serine 15


Mass: 26379.672 Da / Num. of mol.: 4 / Fragment: CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TMPRSS15, ENTK, PRSS7 / Production host: Escherichia coli (E. coli) / References: UniProt: P98073, enteropeptidase

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Non-polymers , 5 types, 463 molecules

#2: Chemical
ChemComp-GBS / 4-GUANIDINOBENZOIC ACID / Nafamostat


Mass: 179.176 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H9N3O2 / Feature type: SUBJECT OF INVESTIGATION
Comment: anticancer, anticoagulant, antivirus, protease inhibitor*YM
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 451 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.73 Å3/Da / Density % sol: 55.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.25 / Details: PEG20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 2.19→104.31 Å / Num. obs: 59929 / % possible obs: 99.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 35.148 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.107 / Rrim(I) all: 0.126 / Χ2: 1.015 / Net I/σ(I): 9.59
Reflection shellResolution: 2.19→2.44 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 2.91 / Num. unique obs: 16358 / CC1/2: 0.997 / Rrim(I) all: 0.571 / % possible all: 99.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
REFMAC5.8.0155refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 2.19→104.31 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.91 / SU B: 12.861 / SU ML: 0.171 / SU R Cruickshank DPI: 0.2733 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.273 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2504 1502 2.5 %RANDOM
Rwork0.2262 ---
obs0.2268 58427 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 103.08 Å2 / Biso mean: 34.429 Å2 / Biso min: 4.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2--1.43 Å2-0 Å2
3----1.51 Å2
Refinement stepCycle: final / Resolution: 2.19→104.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7386 0 88 453 7927
Biso mean--41.35 31.99 -
Num. residues----938
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0197702
X-RAY DIFFRACTIONr_bond_other_d0.0030.026971
X-RAY DIFFRACTIONr_angle_refined_deg1.5651.9510515
X-RAY DIFFRACTIONr_angle_other_deg1.253316013
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7485958
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.63724.372366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.922151171
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3481546
X-RAY DIFFRACTIONr_chiral_restr0.090.21106
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218925
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021837
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A145420.07
12B145420.07
21A148540.06
22C148540.06
31A147180.06
32D147180.06
41B146360.07
42C146360.07
51B148140.07
52D148140.07
61C147140.07
62D147140.07
LS refinement shellResolution: 2.19→2.247 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 113 -
Rwork0.297 4246 -
all-4359 -
obs--99.57 %
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)
13.0182-0.1173-1.09251.89280.49461.7438-0.0320.00040.0075-0.0338-0.038-0.05090.16250.01860.07010.17740.0053-0.01190.00160.00950.26258.59796.653108.102
21.09950.62590.24333.3049-0.1362.49850.0039-0.0132-0.0988-0.0443-0.01260.07410.0937-0.03890.00870.16450.01180.03450.0292-0.01170.190435.25364.447119.376
33.1953-0.661.19892.62-0.59483.00650.04710.2350.0029-0.1205-0.1626-0.1977-0.02130.17860.11540.18370.0320.04350.04880.03020.292957.90750.52290.91
41.2157-0.458-0.13873.6119-0.25962.3548-0.0019-0.00230.13250.0343-0.02510.1184-0.1906-0.0170.02690.16930.019-0.01670.058-0.01470.19633.48682.79381.851
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C1 - 300
2X-RAY DIFFRACTION2B1 - 300
3X-RAY DIFFRACTION3A1 - 300
4X-RAY DIFFRACTION4D1 - 300

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