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- PDB-5qac: OXA-48 IN COMPLEX WITH COMPOUND 6c -

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Basic information

Entry
Database: PDB / ID: 5qac
TitleOXA-48 IN COMPLEX WITH COMPOUND 6c
ComponentsBeta-lactamase
KeywordsHYDROLASE / Oxacillinase / Inhibitor / Complex / OXA / Antibiotic resistance / beta-lactamase / fragment
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / metal ion binding
Similarity search - Function
Beta-lactamase, class-D active site / Beta-lactamase class-D active site. / : / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-(4-methoxyphenyl)benzoic acid / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLund, B.A. / Leiros, H.K.S.
CitationJournal: Eur J Med Chem / Year: 2018
Title: A focused fragment library targeting the antibiotic resistance enzyme - Oxacillinase-48: Synthesis, structural evaluation and inhibitor design.
Authors: Akhter, S. / Lund, B.A. / Ismael, A. / Langer, M. / Isaksson, J. / Christopeit, T. / Leiros, H.S. / Bayer, A.
History
DepositionJul 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Structure summary / Category: pdbx_deposit_group
Item: _pdbx_deposit_group.group_title / _pdbx_deposit_group.group_type
Revision 1.2Mar 14, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.3Nov 17, 2021Group: Database references / Structure summary / Category: database_2 / pdbx_deposit_group
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_deposit_group.group_description
Revision 1.4Nov 15, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / 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: Beta-lactamase
B: Beta-lactamase
C: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,20215
Polymers112,9084
Non-polymers1,29411
Water15,313850
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6155
Polymers28,2271
Non-polymers3884
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6155
Polymers28,2271
Non-polymers3884
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5173
Polymers28,2271
Non-polymers2902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4552
Polymers28,2271
Non-polymers2281
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.161, 106.805, 124.907
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
11(chain A and (resid 25 through 36 or (resid 37...
21(chain B and (resid 25 through 114 or resid 116...
31(chain C and (resid 25 through 36 or (resid 37...
41(chain D and (resid 25 through 36 or (resid 37...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TRPTRPTHRTHR(chain A and (resid 25 through 36 or (resid 37...AA25 - 363 - 14
12GLUGLUGLUGLU(chain A and (resid 25 through 36 or (resid 37...AA3715
13GLUGLUPROPRO(chain A and (resid 25 through 36 or (resid 37...AA24 - 2652 - 243
14GLUGLUPROPRO(chain A and (resid 25 through 36 or (resid 37...AA24 - 2652 - 243
15GLUGLUPROPRO(chain A and (resid 25 through 36 or (resid 37...AA24 - 2652 - 243
16GLUGLUPROPRO(chain A and (resid 25 through 36 or (resid 37...AA24 - 2652 - 243
21TRPTRPALAALA(chain B and (resid 25 through 114 or resid 116...BB25 - 1143 - 92
22LYSLYSLYSLYS(chain B and (resid 25 through 114 or resid 116...BB116 - 13794 - 115
23LEULEUILEILE(chain B and (resid 25 through 114 or resid 116...BB139 - 170117 - 148
24PHEPHETRPTRP(chain B and (resid 25 through 114 or resid 116...BB172 - 225150 - 203
25GLUGLUASNASN(chain B and (resid 25 through 114 or resid 116...BB227 - 231205 - 209
26TRPTRPPROPRO(chain B and (resid 25 through 114 or resid 116...BB233 - 265211 - 243
31TRPTRPTHRTHR(chain C and (resid 25 through 36 or (resid 37...CC25 - 363 - 14
32GLUGLUGLUGLU(chain C and (resid 25 through 36 or (resid 37...CC3715
33GLUGLUPROPRO(chain C and (resid 25 through 36 or (resid 37...CC24 - 2652 - 243
34GLUGLUPROPRO(chain C and (resid 25 through 36 or (resid 37...CC24 - 2652 - 243
35GLUGLUPROPRO(chain C and (resid 25 through 36 or (resid 37...CC24 - 2652 - 243
36GLUGLUPROPRO(chain C and (resid 25 through 36 or (resid 37...CC24 - 2652 - 243
41TRPTRPTHRTHR(chain D and (resid 25 through 36 or (resid 37...DD25 - 363 - 14
42GLUGLUGLUGLU(chain D and (resid 25 through 36 or (resid 37...DD3715
43TRPTRPPROPRO(chain D and (resid 25 through 36 or (resid 37...DD25 - 2653 - 243
44TRPTRPPROPRO(chain D and (resid 25 through 36 or (resid 37...DD25 - 2653 - 243
45TRPTRPPROPRO(chain D and (resid 25 through 36 or (resid 37...DD25 - 2653 - 243
46TRPTRPPROPRO(chain D and (resid 25 through 36 or (resid 37...DD25 - 2653 - 243

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Components

#1: Protein
Beta-lactamase


Mass: 28226.951 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla OXA-48, blaOXA-48, KPE71T_00045 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6XEC0, beta-lactamase
#2: Chemical
ChemComp-U4J / 3-(4-methoxyphenyl)benzoic acid


Mass: 228.243 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H12O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 850 / 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: 2.6 Å3/Da / Density % sol: 52.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 8-11% PEG 8000 and 4-8% 1-butanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87258 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87258 Å / Relative weight: 1
ReflectionResolution: 2→49.1 Å / % possible obs: 99.51 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.108 / Rrim(I) all: 0.12 / Net I/σ(I): 10.73
Reflection shellResolution: 2→2.07 Å / % possible obs: 99.65 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.6465 / Num. unique obs: 38213 / Rrim(I) all: 0.72 / Net I/σ(I) obs: 2.28

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Processing

Software
NameVersionClassificationNB
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY: 5dtk

5dtk


Resolution: 2→49.1 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2155 3994 -
Rwork0.1736 --
obs-79863 99.51 %
Refinement stepCycle: final / Resolution: 2→49.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7919 0 164 850 8933
Biso mean--94.35 37.82 -
Num. residues----967
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048324
X-RAY DIFFRACTIONf_angle_d0.71711276
X-RAY DIFFRACTIONf_chiral_restr0.0491175
X-RAY DIFFRACTIONf_plane_restr0.0041515
X-RAY DIFFRACTIONf_dihedral_angle_d18.2164923
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5976X-RAY DIFFRACTION6.132TORSIONAL
12B5976X-RAY DIFFRACTION6.132TORSIONAL
13C5976X-RAY DIFFRACTION6.132TORSIONAL
14D5976X-RAY DIFFRACTION6.132TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.02350.30541360.263425812717100
2.0235-2.04820.29991320.24826122744100
2.0482-2.07410.30061330.24222547268099
2.0741-2.10140.2691290.22326512780100
2.1014-2.13020.26441420.205825632705100
2.1302-2.16070.23971210.203426162737100
2.1607-2.19290.21451300.19722594272499
2.1929-2.22720.24741300.186925822712100
2.2272-2.26370.23911320.18925972729100
2.2637-2.30270.23261380.177825862724100
2.3027-2.34460.25761340.184726092743100
2.3446-2.38970.23921370.189526192756100
2.3897-2.43850.22681120.172725932705100
2.4385-2.49150.24031370.17492600273799
2.4915-2.54940.21391510.17062593274499
2.5494-2.61320.22051310.166525962727100
2.6132-2.68380.20081480.168825852733100
2.6838-2.76280.22381260.158726232749100
2.7628-2.8520.19131360.160426272763100
2.852-2.95390.19691200.162726412761100
2.9539-3.07210.19671380.165926142752100
3.0721-3.21190.19921360.16726412777100
3.2119-3.38120.19071460.16582622276899
3.3812-3.5930.18281470.163826052752100
3.593-3.87030.18971300.15092648277899
3.8703-4.25960.1871470.14572637278499
4.2596-4.87550.19091550.14752623277899
4.8755-6.14080.22931860.17626582844100
6.1408-49.11780.22731540.20722804295899
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)
11.94641.0332-0.28714.3290.75561.9034-0.0457-0.13120.16910.25920.00840.6743-0.095-0.77440.07910.25480.06040.00210.58260.10340.1873-17.3726-1.545341.3988
26.09973.1278-0.60484.171-0.13792.2282-0.1371-0.15610.09630.19430.06740.0145-0.4133-0.093-0.02830.23440.0189-0.00520.2742-0.01720.1212-8.13050.625938.4058
31.9895-0.761-0.57991.6008-0.14581.8499-0.1062-0.171-0.05760.01740.07790.04620.414-0.06660.0150.2409-0.0527-0.02910.20450.03990.1766-1.7948-13.467135.4286
43.68112.1038-0.53763.0548-0.07671.4498-0.14-0.1694-0.363-0.64060.00870.01240.69080.05230.11780.4717-0.0034-0.00110.18270.01470.27630.9165-24.888816.8759
52.95020.5465-1.46143.2339-0.8191.80580.03970.1447-0.3594-0.10030.2391-0.11650.2417-0.2716-0.32190.3212-0.0614-0.04630.2071-0.00510.1701-5.2659-20.66717.933
62.63090.0535-0.61672.6368-1.06752.7511-0.0508-0.1061-0.1398-0.2881-0.1345-0.35570.3210.14750.12430.2620.00440.00760.15850.05550.22786.9536-21.941632.4962
70.8548-0.51880.07781.7415-0.5172.2688-0.0063-0.15640.04270.209-0.00580.060.0942-0.1240.06520.1933-0.0329-0.02890.22860.02340.18090.8095-11.936436.0139
81.4135-0.6734-0.20621.2769-1.05671.95910.03610.03410.0671-0.07790.0125-0.0410.1335-0.0516-0.06530.1819-0.0419-0.01390.1352-0.01610.1623-1.3717-9.201926.1315
92.35890.8501-0.25112.043-0.01712.44850.1018-0.1579-0.1776-0.00730.01760.31260.2117-0.3567-0.0590.1722-0.0130.00090.22170.05160.1827-8.3684-5.041831.6162
102.5752-0.8969-0.11927.2116-0.36663.46580.0790.2405-0.0403-0.003-0.01930.50930.02-0.3415-0.02480.1551-0.0366-0.00130.32750.06140.2127-16.9179-3.711630.4039
111.4752-0.53550.3471.99680.3281.62290.0433-0.359-0.16170.3074-0.20670.2631-0.2182-0.30480.13740.21290.03270.04890.3445-0.00780.1806-55.63461.810940.6702
121.98310.0360.26711.76960.04043.29750.0774-0.0557-0.1932-0.2713-0.004-0.08140.4564-0.014-0.08030.26370.01780.00350.16450.02750.2157-41.7002-16.638522.9043
130.8291-0.5609-0.21082.1803-0.97631.92270.0251-0.05480.00230.12070.07940.0116-0.09150.0048-0.10120.17510.0043-0.00870.19970.01420.1896-44.6942-5.514830.6867
142.40091.7083-0.34544.299-0.24432.1908-0.10910.0587-0.0931-0.17620.17990.1116-0.1165-0.2953-0.09940.15430.01930.00930.25620.05190.1921-58.6828-0.546731.7279
155.9819-3.1713-1.22775.24921.09523.125-0.27030.4772-0.2225-0.351-0.01390.4922-0.0236-0.10440.22990.2032-0.088-0.00240.23250.01460.1642-58.79052.8932-10.642
163.6131-2.92912.086.1422-2.36433.45530.0188-0.1007-0.3858-0.19470.18420.24510.4279-0.0299-0.13650.234-0.02390.04430.2141-0.02940.2015-51.1721-0.7782-7.0291
171.38210.69041.50141.20680.37342.6798-0.06040.08650.0569-0.07780.035-0.0226-0.0790.20330.06050.1822-0.01910.03690.198-0.0030.2057-40.870811.6844-1.3877
182.4473-2.2645-0.66255.3059-0.10080.4117-0.0717-0.0410.02060.37370.12670.1172-0.0577-0.0099-0.01010.266-0.0649-0.05030.2327-0.06010.2179-38.499721.073316.8915
191.71561.41011.17074.36620.24561.68450.0476-0.19090.11650.44180.1395-0.29270.12710.1937-0.08740.25970.0092-0.00950.2183-0.00460.1808-45.484518.363515.0609
203.3221-1.2674-0.28984.98291.97724.1774-0.09670.06260.0444-0.31170.0714-0.5665-0.26980.31530.05810.1868-0.03070.02160.22250.01580.2394-30.88217.49244.7857
211.0957-0.0689-0.29281.2664-0.79671.6759-0.02410.0718-0.0451-0.1041-0.0541-0.25430.00210.28220.06110.2021-0.00310.02360.2327-0.01050.2291-36.38318.45831.1275
220.8292-0.76770.0274.0245-2.47643.307-0.0884-0.0170.028-0.1490.1199-0.23170.06710.0084-0.13060.1639-0.02150.00010.1582-0.01260.1712-50.12379.90954.5666
231.1528-0.79290.63531.5291-0.05461.4938-0.05680.0004-0.04260.08790.13140.00160.1548-0.0971-0.02540.2262-0.01470.02960.22450.00850.1793-50.49023.82290.8008
241.90460.6436-0.422.1518-0.62992.6139-0.0252-0.0752-0.1294-0.3111-0.01740.05570.2189-0.2084-0.00490.1402-0.0614-0.010.17970.0230.1678-59.13074.61761.1676
250.6164-0.2097-0.16462.135-0.32932.17660.05920.0562-0.0894-0.3136-0.06250.3680.2233-0.49630.02760.2284-0.0047-0.03920.3104-0.01630.2178-7.2424-0.8863-7.6671
263.5026-0.7548-1.24232.86841.70933.814-0.1161-0.1486-0.15950.4186-0.1098-0.17740.3230.23740.17360.19470.0193-0.03190.1290.02410.19711.34387.172214.1718
271.5362-0.49940.28447.98430.63491.9802-0.1296-0.07910.22040.30630.18450.1456-0.23110.0048-0.13190.23420.03250.02790.193-0.00590.1783-0.55216.927915.2201
284.6583-2.1343-1.48283.68161.3622.466-0.01670.12430.1039-0.09230.0416-0.2386-0.01910.1944-0.0280.1378-0.0301-0.02370.14030.02680.172713.035912.88694.9585
290.78760.1168-0.16061.607-0.86941.4041-0.0410.0738-0.0131-0.15090.014-0.08930.14060.01060.03910.17530.00790.01250.186-0.01630.17087.77863.34281.1376
300.4374-0.3738-0.10082.164-0.31921.45880.110.00920.0314-0.0867-0.0530.17150.0274-0.121-0.03080.1544-0.0138-0.01590.22030.00910.1988-6.22121.74892.4743
311.8430.7177-0.11271.8165-0.26652.5884-0.0933-0.2814-0.0860.18790.21620.86510.3002-0.3915-0.150.2225-0.04480.02880.38410.01570.2966-15.0717-0.39381.0578
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 25 through 38 )A25 - 38
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 56 )A39 - 56
3X-RAY DIFFRACTION3chain 'A' and (resid 57 through 82 )A57 - 82
4X-RAY DIFFRACTION4chain 'A' and (resid 83 through 102 )A83 - 102
5X-RAY DIFFRACTION5chain 'A' and (resid 103 through 119 )A103 - 119
6X-RAY DIFFRACTION6chain 'A' and (resid 120 through 155 )A120 - 155
7X-RAY DIFFRACTION7chain 'A' and (resid 156 through 177 )A156 - 177
8X-RAY DIFFRACTION8chain 'A' and (resid 178 through 218 )A178 - 218
9X-RAY DIFFRACTION9chain 'A' and (resid 219 through 243 )A219 - 243
10X-RAY DIFFRACTION10chain 'A' and (resid 244 through 265 )A244 - 265
11X-RAY DIFFRACTION11chain 'B' and (resid 25 through 68 )B25 - 68
12X-RAY DIFFRACTION12chain 'B' and (resid 69 through 141 )B69 - 141
13X-RAY DIFFRACTION13chain 'B' and (resid 142 through 231 )B142 - 231
14X-RAY DIFFRACTION14chain 'B' and (resid 232 through 265 )B232 - 265
15X-RAY DIFFRACTION15chain 'C' and (resid 25 through 38 )C25 - 38
16X-RAY DIFFRACTION16chain 'C' and (resid 39 through 58 )C39 - 58
17X-RAY DIFFRACTION17chain 'C' and (resid 59 through 82 )C59 - 82
18X-RAY DIFFRACTION18chain 'C' and (resid 83 through 102 )C83 - 102
19X-RAY DIFFRACTION19chain 'C' and (resid 103 through 119 )C103 - 119
20X-RAY DIFFRACTION20chain 'C' and (resid 120 through 141 )C120 - 141
21X-RAY DIFFRACTION21chain 'C' and (resid 142 through 194 )C142 - 194
22X-RAY DIFFRACTION22chain 'C' and (resid 195 through 218 )C195 - 218
23X-RAY DIFFRACTION23chain 'C' and (resid 219 through 243 )C219 - 243
24X-RAY DIFFRACTION24chain 'C' and (resid 244 through 265 )C244 - 265
25X-RAY DIFFRACTION25chain 'D' and (resid 25 through 74 )D25 - 74
26X-RAY DIFFRACTION26chain 'D' and (resid 75 through 92 )D75 - 92
27X-RAY DIFFRACTION27chain 'D' and (resid 93 through 119 )D93 - 119
28X-RAY DIFFRACTION28chain 'D' and (resid 120 through 141 )D120 - 141
29X-RAY DIFFRACTION29chain 'D' and (resid 142 through 194 )D142 - 194
30X-RAY DIFFRACTION30chain 'D' and (resid 195 through 243 )D195 - 243
31X-RAY DIFFRACTION31chain 'D' and (resid 244 through 265 )D244 - 265

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