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(-) Description

Title :  CRYSTAL STRUCTURE OF AN ENGINEERED OXA-10 VARIANT WITH CARBAPENEMASE ACTIVITY, OXA-10LOOP24
 
Authors :  F. De Luca, M. Benvenuti, F. Carboni, C. Pozzi, G. M. Rossolini, S. Mang J. D. Docquier
Date :  08 Feb 11  (Deposition) - 02 Nov 11  (Release) - 24 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Antibiotic Resistance, Hydrolysis Of Amide Bond Of Beta-Lactam Compounds, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. De Luca, M. Benvenuti, F. Carboni, C. Pozzi, G. M. Rossolini, S. Mangani, J. D. Docquier
Evolution To Carbapenem-Hydrolyzing Activity In Noncarbapenemase Class D {Beta}-Lactamase Oxa-10 By Rationa Protein Design.
Proc. Natl. Acad. Sci. Usa V. 108 18424 2011
PubMed-ID: 22042844  |  Reference-DOI: 10.1073/PNAS.1110530108

(-) Compounds

Molecule 1 - OXACILLINASE
    ChainsA, B, C, D
    EC Number3.5.2.6
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPLB-II-OXA10LOOP24
    Expression System StrainDH5(ALPHA)
    Expression System Taxid668369
    Expression System Vector TypePLB-II
    FragmentSEE REMARK 999
    GeneBLAOXA-10(LOOP24)
    Organism ScientificESCHERICHIA COLI
    Organism Taxid668369
    StrainDH5(ALPHA)
    SynonymOXA-10LOOP24, OXA-10 LABORATORY VARIANT

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 34)

Asymmetric Unit (3, 34)
No.NameCountTypeFull Name
1EDO23Ligand/Ion1,2-ETHANEDIOL
2KCX4Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
3SO47Ligand/IonSULFATE ION
Biological Unit 1 (3, 18)
No.NameCountTypeFull Name
1EDO12Ligand/Ion1,2-ETHANEDIOL
2KCX2Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
3SO44Ligand/IonSULFATE ION
Biological Unit 2 (3, 16)
No.NameCountTypeFull Name
1EDO11Ligand/Ion1,2-ETHANEDIOL
2KCX2Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
3SO43Ligand/IonSULFATE ION

(-) Sites  (30, 30)

Asymmetric Unit (30, 30)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER D:67 , SER D:115 , LYS D:205 , THR D:206 , GLY D:207 , TRP D:208 , ARG D:250 , HOH D:285 , HOH D:337BINDING SITE FOR RESIDUE SO4 D 1
02AC2SOFTWARESER C:67 , SER C:115 , LYS C:205 , THR C:206 , GLY C:207 , TRP C:208 , ARG C:250 , HOH C:336BINDING SITE FOR RESIDUE SO4 C 2
03AC3SOFTWARESO4 B:5 , THR B:206 , ARG B:250 , HOH B:291 , SER D:147 , GLN D:158BINDING SITE FOR RESIDUE SO4 D 3
04AC4SOFTWARETHR A:206 , ARG A:250 , LYS A:251 , HOH A:304 , HOH A:404 , SER C:147 , GLN C:158BINDING SITE FOR RESIDUE SO4 A 4
05AC5SOFTWARESER B:67 , SER B:115 , LYS B:205 , THR B:206 , GLY B:207 , TRP B:208 , ARG B:250 , HOH B:279 , HOH B:293 , SO4 D:3BINDING SITE FOR RESIDUE SO4 B 5
06AC6SOFTWARESER A:181 , LYS A:182 , HOH A:285 , HOH A:381 , SER B:27BINDING SITE FOR RESIDUE SO4 A 6
07AC7SOFTWARESER A:27 , LYS A:30 , SER B:181 , LYS B:182 , HOH B:276 , HOH B:331BINDING SITE FOR RESIDUE SO4 B 7
08AC8SOFTWARELEU A:43 , LYS A:45 , SER A:50 , ALA A:52 , EDO B:8 , THR B:80 , ARG B:131 , HOH B:359 , HOH B:368BINDING SITE FOR RESIDUE EDO B 1
09AC9SOFTWARETHR A:80 , ARG A:131 , LEU B:43 , SER B:50 , CYS B:51 , ALA B:52 , HOH B:315BINDING SITE FOR RESIDUE EDO A 2
10BC1SOFTWARETHR B:107 , ARG B:109 , HOH B:269 , PRO C:198 , GLU C:199 , GLU C:229BINDING SITE FOR RESIDUE EDO B 3
11BC2SOFTWAREARG A:160 , HOH A:320 , HOH A:327BINDING SITE FOR RESIDUE EDO A 267
12BC3SOFTWARETHR A:107 , ARG A:109 , PRO D:198 , GLU D:199 , GLU D:229BINDING SITE FOR RESIDUE EDO D 5
13BC4SOFTWAREGLU B:195 , ALA B:196 , GLU C:195 , ALA C:196 , HOH D:339BINDING SITE FOR RESIDUE EDO C 6
14BC5SOFTWAREGLU B:227 , GLU B:229 , THR C:107 , ARG C:109BINDING SITE FOR RESIDUE EDO C 7
15BC6SOFTWARELEU A:43 , CYS A:44 , LYS A:45 , TYR A:233 , GLU A:261 , ILE A:263 , EDO B:1 , ARG B:131 , HOH B:359BINDING SITE FOR RESIDUE EDO B 8
16BC7SOFTWAREGLU A:195 , ALA A:196 , HOH C:330 , GLU D:195 , ALA D:196BINDING SITE FOR RESIDUE EDO A 9
17BC8SOFTWAREPHE A:139 , GLU A:168 , SER A:172 , LEU A:178 , HOH A:288BINDING SITE FOR RESIDUE EDO A 10
18BC9SOFTWAREARG C:58 , LYS C:61 , HOH C:312 , ALA D:36 , ASN D:38 , HOH D:328BINDING SITE FOR RESIDUE EDO D 11
19CC1SOFTWAREGLU A:129 , VAL A:130 , GLN A:133 , HOH A:301 , HOH A:313BINDING SITE FOR RESIDUE EDO A 12
20CC2SOFTWAREHOH D:12 , LYS D:138 , PHE D:139 , GLU D:168 , PHE D:169 , SER D:172BINDING SITE FOR RESIDUE EDO D 13
21CC3SOFTWARETYR B:174 , HOH B:214 , GLU B:227 , THR B:230 , HOH B:280 , HOH B:335 , HOH B:481 , THR C:107BINDING SITE FOR RESIDUE EDO B 14
22CC4SOFTWAREGLU A:229 , THR D:107 , ARG D:109 , HOH D:392BINDING SITE FOR RESIDUE EDO D 15
23CC5SOFTWARELEU A:175 , ASN A:176 , LYS A:182 , HOH D:487BINDING SITE FOR RESIDUE EDO A 16
24CC6SOFTWAREASN B:85 , HIS B:87 , LEU C:175 , ASN C:176 , LYS C:182BINDING SITE FOR RESIDUE EDO C 17
25CC7SOFTWAREPHE B:139 , GLU B:168 , SER B:172 , LEU B:178 , HOH B:281 , HOH B:283BINDING SITE FOR RESIDUE EDO B 18
26CC8SOFTWAREPHE C:139 , GLU C:168 , SER C:172 , LEU C:178 , HOH C:269BINDING SITE FOR RESIDUE EDO C 19
27CC9SOFTWAREGLU C:195 , TYR C:200 , VAL C:202 , TRP C:222 , THR C:255 , ILE C:264 , HOH C:272BINDING SITE FOR RESIDUE EDO C 20
28DC1SOFTWARETYR A:174 , THR A:230 , HOH A:291 , HOH A:331 , HOH A:491 , THR D:107BINDING SITE FOR RESIDUE EDO A 268
29DC2SOFTWAREALA C:36 , ASN C:38 , ARG D:58 , LYS D:61 , HOH D:330 , HOH D:388BINDING SITE FOR RESIDUE EDO C 267
30DC3SOFTWAREASN A:85 , HIS A:87 , ASN D:176 , LYS D:182BINDING SITE FOR RESIDUE EDO D 267

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:44 -A:51
2B:44 -B:51
3C:44 -C:51
4D:44 -D:51

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Thr A:213 -Pro A:217
2Thr B:213 -Pro B:217
3Thr C:213 -Pro C:217
4Thr D:213 -Pro D:217

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QNB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3QNB)

(-) Exons   (0, 0)

(no "Exon" information available for 3QNB)

(-) 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:242
 aligned with Q7BNC2_ECOLX | Q7BNC2 from UniProtKB/TrEMBL  Length:266

    Alignment length:245
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260     
         Q7BNC2_ECOLX    21 SITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIG 265
               SCOP domains d3qnba_ A: automated matches                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.hhhhhhhhh....eeeeeee.....eee.hhhhhh.ee.hhhhhhhhhhhhhhhh..................hhhhh...hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.....................eehhhhhhhhhhhhh.....hhhhhhhhhhhheeee...eeeeeeeee-e....--.eeeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qnb A  21 SITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFkIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGW-GMGVT--PQVGWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIG 265
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       209   |  |220       230       240       250       260     
                                                                            70-KCX                                                                                                                                   208 | 213  |                                                
                                                                                                                                                                                                                       209    217                                                

Chain B from PDB  Type:PROTEIN  Length:242
 aligned with Q7BNC2_ECOLX | Q7BNC2 from UniProtKB/TrEMBL  Length:266

    Alignment length:245
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260     
         Q7BNC2_ECOLX    21 SITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIG 265
               SCOP domains d3qnbb_ B: automated matches                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.hhhhhhhhh....eeeeeee.....eee.hhhhhh.ee.hhhhhhhhhhhhhhhh........ee........hhhhh..eehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.....................eehhhhhhhhhhhhh.....hhhhhhhhhhhheeee...eeeeeeeee-e....--.eeeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qnb B  21 SITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFkIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGW-GMGVT--PQVGWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIG 265
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       209   |  |220       230       240       250       260     
                                                                            70-KCX                                                                                                                                   208 | 213  |                                                
                                                                                                                                                                                                                       209    217                                                

Chain C from PDB  Type:PROTEIN  Length:242
 aligned with Q7BNC2_ECOLX | Q7BNC2 from UniProtKB/TrEMBL  Length:266

    Alignment length:245
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260     
         Q7BNC2_ECOLX    21 SITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIG 265
               SCOP domains d3qnbc_ C: automated matches                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.hhhhhhhhh....eeeeeee.....eee.hhhhhhhee.hhhhhhhhhhhhhhhh..................hhhhh...hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.....................eehhhhhhhhhhhhh.....hhhhhhhhhhhheeeee..eeeeeeeee-e....--.eeeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qnb C  21 SITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFkIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGW-GMGVT--PQVGWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIG 265
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       209   |  |220       230       240       250       260     
                                                                            70-KCX                                                                                                                                   208 | 213  |                                                
                                                                                                                                                                                                                       209    217                                                

Chain D from PDB  Type:PROTEIN  Length:241
 aligned with Q7BNC2_ECOLX | Q7BNC2 from UniProtKB/TrEMBL  Length:266

    Alignment length:244
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261    
         Q7BNC2_ECOLX    22 ITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIG 265
               SCOP domains d3qnbd_ D: automated matches                                                                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...hhhhhhh....eeeeeee.....eee.hhhhhh.ee.hhhhhhhhhhhhhhhh..................hhhhh...hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.....................eehhhhhhhhhhhhh.....hhhhhhhhhhhheeeee..eeeeeeeee-e....--.eeeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qnb D  22 ITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFkIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGW-GMGVT--PQVGWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIG 265
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201      |210  |  | 221       231       241       251       261    
                                                                           70-KCX                                                                                                                                   208 | 213  |                                                
                                                                                                                                                                                                                      209    217                                                

   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, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3QNB)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3QNB)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q7BNC2_ECOLX | Q7BNC2)
molecular function
    GO:0008800    beta-lactamase activity    Catalysis of the reaction: a beta-lactam + H2O = a substituted beta-amino acid.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008658    penicillin binding    Interacting selectively and non-covalently with penicillin, any antibiotic that contains the condensed beta-lactamthiazolidine ring system.
biological process
    GO:0017001    antibiotic catabolic process    The chemical reactions and pathways resulting in the breakdown of antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
    GO:0046677    response to antibiotic    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.

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        Q7BNC2_ECOLX | Q7BNC23qnc

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3qnc