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- PDB-3kqx: Structure of a protease 1 -

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Basic information

Entry
Database: PDB / ID: 3kqx
TitleStructure of a protease 1
ComponentsM17 leucyl aminopeptidase
KeywordsHYDROLASE / protease / Aminopeptidase
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Dipeptidases / leucyl aminopeptidase / metallodipeptidase activity / peptide catabolic process / metalloaminopeptidase activity / carboxypeptidase activity / peptidase activity / manganese ion binding / proteolysis / zinc ion binding ...Hydrolases; Acting on peptide bonds (peptidases); Dipeptidases / leucyl aminopeptidase / metallodipeptidase activity / peptide catabolic process / metalloaminopeptidase activity / carboxypeptidase activity / peptidase activity / manganese ion binding / proteolysis / zinc ion binding / metal ion binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Peptidase M17, leucine aminopeptidase / Cytosol aminopeptidase signature. / Peptidase M17, leucyl aminopeptidase, C-terminal / Peptidase M17, leucine aminopeptidase/peptidase B / Cytosol aminopeptidase family, catalytic domain / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Zn peptidases / Aminopeptidase / Macro domain-like ...Peptidase M17, leucine aminopeptidase / Cytosol aminopeptidase signature. / Peptidase M17, leucyl aminopeptidase, C-terminal / Peptidase M17, leucine aminopeptidase/peptidase B / Cytosol aminopeptidase family, catalytic domain / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Zn peptidases / Aminopeptidase / Macro domain-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CARBONATE ION / Leucine aminopeptidase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsMcGowan, S. / Whisstock, J.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structure of the Plasmodium falciparum M17 aminopeptidase and significance for the design of drugs targeting the neutral exopeptidases
Authors: McGowan, S. / Oellig, C.A. / Birru, W.A. / Caradoc-Davies, T.T. / Stack, C.M. / Lowther, J. / Skinner-Adams, T. / Mucha, A. / Kafarski, P. / Grembecka, J. / Trenholme, K.R. / Buckle, A.M. / ...Authors: McGowan, S. / Oellig, C.A. / Birru, W.A. / Caradoc-Davies, T.T. / Stack, C.M. / Lowther, J. / Skinner-Adams, T. / Mucha, A. / Kafarski, P. / Grembecka, J. / Trenholme, K.R. / Buckle, A.M. / Gardiner, D.L. / Dalton, J.P. / Whisstock, J.C.
History
DepositionNov 17, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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 / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: M17 leucyl aminopeptidase
B: M17 leucyl aminopeptidase
C: M17 leucyl aminopeptidase
D: M17 leucyl aminopeptidase
E: M17 leucyl aminopeptidase
F: M17 leucyl aminopeptidase
G: M17 leucyl aminopeptidase
H: M17 leucyl aminopeptidase
I: M17 leucyl aminopeptidase
J: M17 leucyl aminopeptidase
K: M17 leucyl aminopeptidase
L: M17 leucyl aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)722,075110
Polymers704,50812
Non-polymers17,56798
Water62,0263443
1
A: M17 leucyl aminopeptidase
B: M17 leucyl aminopeptidase
C: M17 leucyl aminopeptidase
D: M17 leucyl aminopeptidase
E: M17 leucyl aminopeptidase
F: M17 leucyl aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)361,02556
Polymers352,2546
Non-polymers8,77150
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27020 Å2
ΔGint-129 kcal/mol
Surface area97620 Å2
MethodPISA
2
G: M17 leucyl aminopeptidase
H: M17 leucyl aminopeptidase
I: M17 leucyl aminopeptidase
J: M17 leucyl aminopeptidase
K: M17 leucyl aminopeptidase
L: M17 leucyl aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)361,04954
Polymers352,2546
Non-polymers8,79648
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26940 Å2
ΔGint-129 kcal/mol
Surface area97670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.404, 176.809, 224.246
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21G
12B
22H
13C
23I
14D
24J
15E
25K

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 1 / Auth seq-ID: 86 - 602 / Label seq-ID: 3 - 519

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21GG
12BB
22HH
13CC
23II
14DD
24JJ
15EE
25KK

NCS ensembles :
ID
1
2
3
4
5

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
M17 leucyl aminopeptidase / Malarial protease


Mass: 58708.973 Da / Num. of mol.: 12 / Fragment: residues 84-605 / Mutation: N152Q, N515Q, N546Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Plasmid: pTrc-His2b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 DE3 Rosetta2 / References: UniProt: Q8IL11, leucyl aminopeptidase

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Non-polymers , 6 types, 3541 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CO3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#5: Chemical...
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 54 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical
ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3443 / 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: 2.44 Å3/Da / Density % sol: 49.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 40% PEG 400, 0.1M Tris pH 8.5, 0.2M LiSO4, 1mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.96181 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 24, 2009
RadiationMonochromator: Double Crystal silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96181 Å / Relative weight: 1
ReflectionResolution: 2→57.26 Å / Num. obs: 455194 / % possible obs: 100 % / Redundancy: 24.5 % / Rmerge(I) obs: 0.369 / Rsym value: 0.075 / Net I/σ(I): 11.1 / Num. measured all: 11156121
Reflection shellResolution: 2→2.11 Å / Redundancy: 24.5 % / Rmerge(I) obs: 1.513 / Mean I/σ(I) obs: 2.6 / Num. unique all: 66073 / Rsym value: 0.31 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GYT

1gyt


Resolution: 2.01→56.08 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.935 / Occupancy max: 1 / Occupancy min: 0 / SU B: 9.064 / SU ML: 0.114 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23174 22865 5 %RANDOM
Rwork0.18029 ---
obs0.18288 432299 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 128.11 Å2 / Biso mean: 16.667 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--1.98 Å20 Å20 Å2
2---0.46 Å20 Å2
3---2.46 Å2
Refinement stepCycle: LAST / Resolution: 2.01→56.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms46722 0 758 3443 50923
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.02248275
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8041.96965261
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.53356107
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.0525.1791902
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.525157844
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.15515100
X-RAY DIFFRACTIONr_chiral_restr0.1470.27487
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02135518
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.753230468
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.126548868
X-RAY DIFFRACTIONr_scbond_it5.588717807
X-RAY DIFFRACTIONr_scangle_it7.8981016393
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A3925TIGHT POSITIONAL0.080.05
1A3925TIGHT THERMAL0.330.5
2B3859TIGHT POSITIONAL0.050.05
2B3859TIGHT THERMAL0.270.5
3C3921TIGHT POSITIONAL0.050.05
3C3921TIGHT THERMAL0.330.5
4D3921TIGHT POSITIONAL0.080.05
4D3921TIGHT THERMAL0.340.5
5E3881TIGHT POSITIONAL0.080.05
5E3881TIGHT THERMAL0.390.5
LS refinement shellResolution: 2.006→2.058 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 1596 -
Rwork0.248 30506 -
all-32102 -
obs--95.75 %
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)
10.4548-0.1321-0.12030.19270.01940.1454-0.0225-0.088-0.00610.04850.0337-0.02250.00190.0069-0.01130.06180.0096-0.01020.0579-0.00180.006674.38882.24940.367
20.3651-0.041-0.00370.36710.07950.3915-0.0117-0.06580.06380.0270.0407-0.1750.03850.0672-0.0290.03210.00080.00390.0358-0.0260.1031120.04768.90113.954
30.3029-0.1944-0.16260.38240.10380.27050.01090.0326-0.0503-0.0491-0.0390.04020.0086-0.03980.0280.0436-0.0043-0.0040.04380.00050.009871.5657.931-8.377
40.481-0.1149-0.17570.25590.06050.2699-0.0035-0.0162-0.01570.03120.00180.047-0.0141-0.03050.00160.0478-0.00890.01750.05910.01980.021257.46841.29427.233
50.33950.08440.02410.35340.12820.4327-0.03780.0133-0.0189-0.01640.0487-0.0077-0.02290.0303-0.01080.03110.00650.00930.02710.00670.0049106.04230.3856.094
60.7122-0.13150.0120.52640.04380.1796-0.0544-0.16040.07560.11280.0581-0.1026-0.00620.0473-0.00360.13990.0421-0.02160.159500.0279102.48455.02554.418
70.4611-0.1424-0.04280.30650.06540.1869-0.0156-0.0635-0.02850.04380.0307-0.02560.0038-0.0224-0.0150.05420.0173-0.01640.02520.00380.011376.2382.253152.502
80.4808-0.0577-0.06750.41320.08290.3819-0.001-0.04450.07550.01830.0482-0.21380.0290.0667-0.04710.0303-0.00040.01430.0211-0.02880.1417121.84468.903125.981
90.3919-0.1761-0.02140.44790.06260.36950.03860.0994-0.0429-0.0864-0.05250.00980.0352-0.00410.01380.05580.009-0.00120.0756-0.00080.007373.28757.758103.946
100.4232-0.0736-0.12450.36860.08020.3073-0.0082-0.0067-0.01020.0251-0.00070.0724-0.0294-0.06120.00890.0435-0.010.00020.05450.0110.016959.27541.231139.668
110.42050.04710.0280.40620.23950.5382-0.0180.06720.0105-0.0620.0502-0.0592-0.06060.0163-0.03220.0339-0.00010.01280.0248-0.00230.0126107.86430.331118.435
120.514-0.10310.0120.47560.00530.27-0.0466-0.0240.07130.08560.0365-0.1031-0.01420.03820.010.09530.03-0.03690.0565-0.00140.0338104.36655.178166.553
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A86 - 603
2X-RAY DIFFRACTION2B86 - 603
3X-RAY DIFFRACTION3C86 - 603
4X-RAY DIFFRACTION4D86 - 603
5X-RAY DIFFRACTION5E86 - 602
6X-RAY DIFFRACTION6F86 - 603
7X-RAY DIFFRACTION7G86 - 603
8X-RAY DIFFRACTION8H86 - 603
9X-RAY DIFFRACTION9I86 - 603
10X-RAY DIFFRACTION10J86 - 603
11X-RAY DIFFRACTION11K86 - 602
12X-RAY DIFFRACTION12L86 - 603

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