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- PDB-2r0l: Short Form HGFA with Inhibitory Fab75 -

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Basic information

Entry
Database: PDB / ID: 2r0l
TitleShort Form HGFA with Inhibitory Fab75
Components
  • (Hepatocyte growth factor ...) x 2
  • antibody heavy chain, Fab portion onlyImmunoglobulin heavy chain
  • antibody light chainImmunoglobulin light chain
KeywordsHYDROLASE / IMMUNE SYSTEM / serine protease / antibody / allosteric inhibitor / EGF-like domain / Glycoprotein / Kringle / Secreted / Zymogen
Function / homology
Function and homology information


MET Receptor Activation / zymogen activation / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / rough endoplasmic reticulum / serine-type peptidase activity / blood coagulation / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / cytosol
Similarity search - Function
Coagulation factor XII/hepatocyte growth factor activator / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. ...Coagulation factor XII/hepatocyte growth factor activator / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / EGF-like domain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Epidermal growth factor-like domain. / Kringle-like fold / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / 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 / Immunoglobulins / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Hepatocyte growth factor activator
Similarity search - Component
Biological speciesHomo sapiens (human)
Synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsEigenbrot, C. / Shia, S.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structural insight into distinct mechanisms of protease inhibition by antibodies.
Authors: Wu, Y. / Eigenbrot, C. / Liang, W.C. / Stawicki, S. / Shia, S. / Fan, B. / Ganesan, R. / Lipari, M.T. / Kirchhofer, D.
History
DepositionAug 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 25, 2013Group: Source and taxonomy
Revision 1.3Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 400COMPOUND CHAINS A AND B ARE PART OF THE HGFA SEQUENCE. IN THE MATURE PROTEIN STUDIED HERE, A ...COMPOUND CHAINS A AND B ARE PART OF THE HGFA SEQUENCE. IN THE MATURE PROTEIN STUDIED HERE, A PEPTIDE BOND HAS BEEN BROKEN AND THE TWO SEGMENTS REMAIN CONNECTED BY A DISULFIDE BOND.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: antibody light chain
H: antibody heavy chain, Fab portion only
A: Hepatocyte growth factor activator
B: Hepatocyte growth factor activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,0805
Polymers77,4934
Non-polymers5871
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.820, 48.230, 97.050
Angle α, β, γ (deg.)98.39, 96.24, 100.77
Int Tables number1
Space group name H-MP1

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Components

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Hepatocyte growth factor ... , 2 types, 2 molecules AB

#3: Protein Hepatocyte growth factor activator


Mass: 26940.518 Da / Num. of mol.: 1 / Fragment: short form HGFA
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HGFAC / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q04756, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#4: Protein/peptide Hepatocyte growth factor activator


Mass: 3962.654 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HGFAC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q04756

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Antibody , 2 types, 2 molecules LH

#1: Antibody antibody light chain / Immunoglobulin light chain


Mass: 23287.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens, Synthetic construct
Description: The protein was made using a synthetically diversified gene library and selected for tight binding to a specific target on a plastic surface. The gene library used cloned human genes as its basis
Production host: Escherichia coli (E. coli)
#2: Antibody antibody heavy chain, Fab portion only / Immunoglobulin heavy chain


Mass: 23302.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens, Synthetic construct
Description: The protein was made using a synthetically diversified gene library and selected for tight binding to a specific target on a plastic surface. The gene library used cloned human genes as its basis
Production host: Escherichia coli (E. coli)

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Sugars / Non-polymers , 2 types, 200 molecules

#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O

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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: 2.26 Å3/Da / Density % sol: 45.49 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.5
Details: 1:1 mixture of protein complex solution at 15 mg/mL and reservoir containing 20% PEG 10000, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
RadiationMonochromator: Silicon 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 32514 / Num. obs: 32514 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 1.9 % / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 3
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 3 / Num. unique all: 2563 / % possible all: 74.5

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Processing

Software
NameVersionClassification
REFMAC5.1.07refinement
Blu-IceIcedata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb 1YC0, pdb 1FVD

1yc0

1fvd


Resolution: 2.2→47.51 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.917 / SU B: 6.834 / SU ML: 0.171 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -2 / ESU R: 0.33 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24797 1535 4.7 %RANDOM
Rwork0.19278 ---
all0.195 32514 --
obs0.19537 30979 94.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å2-0.01 Å2-0.1 Å2
2---0.62 Å2-0.44 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.2→47.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5179 0 39 199 5417
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0215376
X-RAY DIFFRACTIONr_angle_refined_deg1.1641.9517331
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.885681
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.92723.732209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.98415813
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9751523
X-RAY DIFFRACTIONr_chiral_restr0.0780.2817
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024054
X-RAY DIFFRACTIONr_nbd_refined0.2040.22114
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2300
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.28
X-RAY DIFFRACTIONr_mcbond_it2.3692.53396
X-RAY DIFFRACTIONr_mcangle_it3.69755481
X-RAY DIFFRACTIONr_scbond_it2.8642.51980
X-RAY DIFFRACTIONr_scangle_it4.21751850
LS refinement shellResolution: 2.2→2.319 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.286 180
Rwork0.222 3758
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)
11.0868-0.21351.01181.37730.33122.95120.11940.0616-0.0512-0.16730.0071-0.01860.3380.0082-0.12640.34170.0615-0.05760.1953-0.04350.1904-19.499-23.64126.992
21.47871.1757-0.70323.0906-1.73912.98980.04580.17290.07180.2190.08520.0079-0.3661-0.1565-0.13110.50810.257-0.07310.1856-0.04240.0394-15.605-1.613-2.41
31.11630.10630.45771.3366-0.23122.2727-0.0650.04420.01730.0350.0607-0.0575-0.08510.04530.00430.27220.0707-0.03490.2278-0.05270.2085-10.542-6.30738.647
43.98991.41212.80315.04610.58143.32650.06560.05780.4111-0.8859-0.29280.551-0.37590.01460.22720.47570.2264-0.08310.1565-0.09380.1439-19.9297.1159.972
50.8729-0.31810.10791.80720.0771.4585-0.0631-0.0755-0.02270.09890.0377-0.0005-0.0077-0.02650.02540.27440.138-0.04880.2377-0.03410.1518-9.868-26.58663.279
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1LA1 - 1101 - 110
2X-RAY DIFFRACTION2LA111 - 214111 - 214
3X-RAY DIFFRACTION3HB1 - 1101 - 114
4X-RAY DIFFRACTION4HB111 - 216115 - 220
5X-RAY DIFFRACTION5AC16 - 2431 - 239

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