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(-) Description

Title :  T4 LYSOZYME L99A/M102H WITH NITROBENZENE BOUND
 
Authors :  M. Merski, B. K. Shoichet
Date :  09 Apr 12  (Deposition) - 05 Sep 12  (Release) - 17 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.64
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A (1x),B (1x)
Keywords :  Hydrolase, Alkylation Of Cys97 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Merski, B. K. Shoichet
Engineering A Model Protein Cavity To Catalyze The Kemp Elimination.
Proc. Natl. Acad. Sci. Usa V. 109 16179 2012
PubMed-ID: 22988064  |  Reference-DOI: 10.1073/PNAS.1208076109

(-) Compounds

Molecule 1 - LYSOZYME
    Chains: A, B
    EC Number: 3.2.1.17
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: E
    Mutation: YES
    Organism Scientific: ENTEROBACTERIA PHAGE T4
    Organism Taxid: 10665
    Synonym: ENDOLYSIN, LYSIS PROTEIN, MURAMIDASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 15)

Asymmetric Unit (5, 15)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2BME4Ligand/IonBETA-MERCAPTOETHANOL
3HED1Ligand/Ion2-HYDROXYETHYL DISULFIDE
4NBZ2Ligand/IonNITROBENZENE
5SO45Ligand/IonSULFATE ION
Biological Unit 1 (4, 8)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2BME2Ligand/IonBETA-MERCAPTOETHANOL
3HED-1Ligand/Ion2-HYDROXYETHYL DISULFIDE
4NBZ1Ligand/IonNITROBENZENE
5SO43Ligand/IonSULFATE ION
Biological Unit 2 (5, 7)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2BME2Ligand/IonBETA-MERCAPTOETHANOL
3HED1Ligand/Ion2-HYDROXYETHYL DISULFIDE
4NBZ1Ligand/IonNITROBENZENE
5SO42Ligand/IonSULFATE ION
Biological Unit 3 (4, 8)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2BME2Ligand/IonBETA-MERCAPTOETHANOL
3HED-1Ligand/Ion2-HYDROXYETHYL DISULFIDE
4NBZ1Ligand/IonNITROBENZENE
5SO43Ligand/IonSULFATE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREILE A:3 , TYR A:88 , ALA A:93 , ARG A:96 , CYS A:97 , ILE A:100 , HOH A:351 , HOH A:436BINDING SITE FOR RESIDUE BME A 201
02AC2SOFTWAREILE A:78 , LEU A:84 , VAL A:87 , TYR A:88 , ALA A:99 , HIS A:102 , VAL A:111 , LEU A:118 , LEU A:121 , PHE A:153BINDING SITE FOR RESIDUE NBZ A 202
03AC3SOFTWAREARG A:14 , LEU A:15 , LYS A:16 , HOH A:319 , HOH A:423BINDING SITE FOR RESIDUE SO4 A 203
04AC4SOFTWAREARG A:76 , ARG A:80 , HOH A:414 , LYS B:135BINDING SITE FOR RESIDUE SO4 A 204
05AC5SOFTWAREARG A:119 , ARG A:125 , LYS B:48BINDING SITE FOR RESIDUE SO4 A 205
06AC6SOFTWAREGLU A:5 , HOH A:468 , HOH B:402BINDING SITE FOR RESIDUE ACT A 206
07AC7SOFTWAREPHE A:-3 , TYR A:161 , HOH A:308 , HOH A:470 , ASN B:55 , HOH B:336BINDING SITE FOR RESIDUE BME A 207
08AC8SOFTWARELYS A:135 , ARG B:76 , ARG B:80 , SO4 B:203 , HOH B:392BINDING SITE FOR RESIDUE ACT A 208
09AC9SOFTWAREILE B:3 , CYS B:97 , HOH B:351BINDING SITE FOR RESIDUE BME B 201
10BC1SOFTWAREILE B:78 , LEU B:84 , VAL B:87 , TYR B:88 , ALA B:99 , HIS B:102 , VAL B:111 , LEU B:121 , PHE B:153BINDING SITE FOR RESIDUE NBZ B 202
11BC2SOFTWAREACT A:208 , ARG B:76 , ARG B:80 , HOH B:346BINDING SITE FOR RESIDUE SO4 B 203
12BC3SOFTWAREARG B:119 , MET B:120 , ARG B:125BINDING SITE FOR RESIDUE SO4 B 204
13BC4SOFTWARELEU B:15 , LYS B:16 , HOH B:433BINDING SITE FOR RESIDUE ACT B 205
14BC5SOFTWAREGLY B:30 , LEU B:32 , ASP B:70 , PHE B:104 , HOH B:331 , HOH B:343 , HOH B:450BINDING SITE FOR RESIDUE BME B 206
15BC6SOFTWARETHR A:109 , HOH A:367 , ALA B:130 , THR B:151 , ARG B:154 , HOH B:368 , HOH B:432BINDING SITE FOR RESIDUE HED B 207

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:21 -A:142
2B:21 -B:142

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4EKP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4EKP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4EKP)

(-) Exons   (0, 0)

(no "Exon" information available for 4EKP)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:175
                                                                                                                                                                                                               
               SCOP domains d4ekpa_ A: Phage T4 lysozyme                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhh.eeeeee.....eeee..ee.....hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ekp A -10 PTTENLYFQGSMNIFEMLRIDEGLRLKIYKDCEGYYTIGIGHLLTKSPDLNAAKSELDKAIGRNCNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRCAAINHVFQMGVTGVAGFTNVLRMLQQKRWDEAAVNLAKSRWYNQCPDRAKRVITTFRTGTWDAYKNL 164
                                    -1         9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159     


Chain B from PDB  Type:PROTEIN  Length:174
                                                                                                                                                                                                              
               SCOP domains d4ekpb_ B: Phage T4 lysozyme                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh.eeeeee.....eeee..ee.....hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ekp B  -9 TTENLYFQGSMNIFEMLRIDEGLRLKIYKDCEGYYTIGIGHLLTKSPDLNAAKSELDKAIGRNCNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRCAAINHVFQMGVTGVAGFTNVLRMLQQKRWDEAAVNLAKSRWYNQCPDRAKRVITTFRTGTWDAYKNL 164
                                     0        10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4EKP)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4EKP)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)

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  3.2.1.17
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UniProtKB/Swiss-Prot
        ENLYS_BPT4 | P00720: 102l 103l 104l 107l 108l 109l 110l 111l 112l 113l 114l 115l 118l 119l 120l 122l 123l 125l 126l 127l 128l 129l 130l 131l 137l 138l 139l 140l 141l 142l 143l 144l 145l 146l 147l 148l 149l 150l 151l 152l 155l 156l 157l 158l 159l 160l 161l 162l 163l 164l 165l 166l 167l 168l 169l 170l 171l 172l 173l 174l 175l 176l 177l 178l 180l 181l 182l 183l 184l 185l 186l 187l 188l 189l 190l 191l 192l 195l 196l 197l 198l 199l 1b6i 1c60 1c61 1c62 1c63 1c64 1c65 1c66 1c67 1c68 1c69 1c6a 1c6b 1c6c 1c6d 1c6e 1c6f 1c6g 1c6h 1c6i 1c6j 1c6k 1c6l 1c6m 1c6n 1c6p 1c6q 1c6t 1ctw 1cu0 1cu2 1cu3 1cu5 1cu6 1cup 1cuq 1cv0 1cv1 1cv3 1cv4 1cv5 1cv6 1cvk 1cx6 1cx7 1d2w 1d2y 1d3f 1d3j 1d3m 1d3n 1d9w 1dya 1dyb 1dyc 1dyd 1dye 1dyf 1dyg 1epy 1g06 1g07 1g0g 1g0j 1g0k 1g0l 1g0m 1g0p 1g0q 1g1v 1g1w 1i6s 1jqu 1jtm 1jtn 1kni 1ks3 1kw5 1kw7 1ky0 1ky1 1l00 1l01 1l02 1l03 1l04 1l05 1l06 1l07 1l08 1l09 1l0j 1l0k 1l10 1l11 1l12 1l13 1l14 1l15 1l16 1l17 1l18 1l19 1l20 1l21 1l22 1l23 1l24 1l25 1l26 1l27 1l28 1l29 1l30 1l31 1l32 1l33 1l34 1l35 1l36 1l37 1l38 1l39 1l40 1l41 1l42 1l43 1l44 1l45 1l46 1l47 1l48 1l49 1l50 1l51 1l52 1l53 1l54 1l55 1l56 1l57 1l58 1l59 1l60 1l61 1l62 1l63 1l64 1l65 1l66 1l67 1l68 1l69 1l70 1l71 1l72 1l73 1l74 1l75 1l76 1l77 1l79 1l80 1l81 1l82 1l83 1l84 1l85 1l86 1l87 1l88 1l89 1l90 1l91 1l92 1l93 1l94 1l95 1l96 1l97 1l98 1l99 1lgu 1lgw 1lgx 1li2 1li3 1li6 1llh 1lpy 1lw9 1lwg 1lwk 1lyd 1lye 1lyf 1lyg 1lyh 1lyi 1lyj 1nhb 1ov5 1ov7 1ovh 1ovj 1ovk 1owy 1owz 1oyu 1p2l 1p2r 1p36 1p37 1p3n 1p46 1p56 1p5c 1p64 1p6y 1p7s 1pqd 1pqi 1pqj 1pqk 1pqm 1pqo 1qs5 1qs9 1qsb 1qsq 1qt3 1qt4 1qt5 1qt6 1qt7 1qt8 1qtb 1qtc 1qtd 1qth 1qtv 1qtz 1qud 1qug 1quh 1quo 1ssw 1ssy 1swy 1swz 1sx2 1sx7 1t6h 1t8a 1t8f 1t8g 1t97 1tla 1xep 1zur 1zwn 1zyt 200l 201l 205l 206l 209l 210l 211l 212l 213l 214l 215l 216l 217l 218l 219l 220l 221l 222l 223l 224l 225l 226l 227l 228l 229l 230l 231l 232l 233l 234l 235l 236l 237l 238l 239l 240l 241l 242l 243l 244l 245l 246l 247l 248l 249l 250l 251l 252l 253l 254l 255l 256l 257l 258l 259l 260l 261l 262l 2a4t 2b6t 2b6w 2b6x 2b6y 2b6z 2b70 2b72 2b73 2b74 2b75 2b7x 2cuu 2f2q 2f32 2f47 2huk 2hul 2hum 2igc 2l78 2lc9 2lcb 2lzm 2ntg 2nth 2o4w 2o79 2o7a 2oe4 2oe7 2oe9 2oea 2oty 2otz 2ou0 2ou8 2ou9 2q9d 2q9e 2qar 2qb0 2ray 2raz 2rb0 2rb1 2rb2 2rbn 2rbo 2rbp 2rbq 2rbr 2rbs 2rh1 3c7w 3c7y 3c7z 3c80 3c81 3c82 3c83 3c8q 3c8r 3c8s 3cdo 3cdq 3cdr 3cdt 3cdv 3d4s 3dke 3dmv 3dmx 3dmz 3dn0 3dn1 3dn2 3dn3 3dn4 3dn6 3dn8 3dna 3eml 3f8v 3f9l 3fa0 3fad 3fi5 3g3v 3g3w 3g3x 3gui 3guj 3guk 3gul 3gum 3gun 3guo 3gup 3hh3 3hh4 3hh5 3hh6 3ht6 3ht7 3ht8 3ht9 3htb 3htd 3htf 3htg 3hu8 3hu9 3hua 3huk 3huq 3hwl 3jr6 3k2r 3l2x 3l64 3lzm 3ny8 3ny9 3nya 3odu 3oe0 3oe6 3oe8 3oe9 3p0g 3pbl 3pds 3qak 3run 3rze 3sb5 3sb6 3sb7 3sb8 3sb9 3sba 3sbb 3sn6 3uon 3v2w 3v2y 3vw7 4arj 4daj 4djh 4dkl 4e97 4ej4 4ekq 4ekr 4eks 4epi 4exm 4gbr 4grv 4htt 4i7j 4i7k 4i7l 4i7m 4i7n 4i7o 4i7p 4i7q 4i7r 4i7s 4i7t 4iap 4k5y 4lde 4ldl 4ldo 4lzm 4n9n 4oo9 4phu 4rws 4s0w 4tn3 4u14 4w51 4w52 4w53 4w54 4w55 4w56 4w57 4w58 4w59 4w8f 4wtv 4xee 4xes 4yx7 4yxa 4yxc 4zwj 5b2g 5cgc 5cgd 5cxv 5d5a 5d5b 5d6l 5dgy 5dsg 5ee7 5eut 5ewx 5g27 5glh 5gli 5i14 5jdt 5jea 5jgn 5jgr 5jgu 5jgv 5jgx 5jgz 5jqh 5jws 5jwt 5jwu 5jwv 5jww 5kgr 5khz 5ki1 5ki2 5ki3 5ki8 5kig 5kii 5kim 5kio 5lwo 5lzm 5t04 5t1a 5tzr 5tzy 5vew 5vex 6lzm 7lzm

(-) Related Entries Specified in the PDB File

4e97 4ekq 4ekr 4eks