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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE MEMBRANE PROTEIN OF UNKNOWN FUNCTION (YFDX) FROM KLEBSIELLA PNEUMONIAE SUBSP. AT 1.65 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  29 Jul 08  (Deposition) - 12 Aug 08  (Release) - 23 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Membrane Protein Of Unknown Function (Yp_001337144. 1) From Klebsiella Pneumoniae Subsp. Pneumoniae Mgh 78578 At 1. 65 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UNCHARACTERIZED PUTATIVE MEMBRANE PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YP_001337144.1, YFDX, KPN78578_34530, KPN_03482
    Organism Scientific: KLEBSIELLA PNEUMONIAE SUBSP. PNEUMONIAE MGH 78578
    Organism Taxid: 272620

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 55)

Asymmetric/Biological Unit (4, 55)
No.NameCountTypeFull Name
1ACT5Ligand/IonACETATE ION
2EDO24Ligand/Ion1,2-ETHANEDIOL
3MSE16Mod. Amino AcidSELENOMETHIONINE
4ZN10Ligand/IonZINC ION

(-) Sites  (39, 39)

Asymmetric Unit (39, 39)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:77 , GLU B:169 , HOH B:590 , HOH B:597 , HOH B:614 , HOH B:624BINDING SITE FOR RESIDUE ZN A 501
02AC2SOFTWAREGLU A:169 , HOH A:547 , HOH A:557 , HOH A:574 , HIS B:77 , HOH B:557BINDING SITE FOR RESIDUE ZN A 502
03AC3SOFTWAREASP A:212 , HOH A:565 , HOH A:578 , ASP D:212 , HOH D:754 , HOH D:764BINDING SITE FOR RESIDUE ZN A 503
04AC4SOFTWAREGLU A:138 , GLU B:138 , HOH B:613 , HOH B:632 , HOH B:760BINDING SITE FOR RESIDUE ZN B 502
05AC5SOFTWAREASP B:212 , HOH B:539 , HOH B:567 , HOH B:576 , ASP C:212 , HOH C:543BINDING SITE FOR RESIDUE ZN B 503
06AC6SOFTWAREEDO A:19 , GLN B:79 , PRO B:80 , ASP B:81 , SER B:82 , HOH B:640BINDING SITE FOR RESIDUE ACT B 1
07AC7SOFTWARETHR A:45 , ASN A:63 , THR B:45 , ASN B:63 , HOH B:510 , HOH B:512 , HOH B:584 , HOH B:656BINDING SITE FOR RESIDUE ACT B 3
08AC8SOFTWAREHIS C:77 , EDO D:16 , GLU D:169 , HOH D:730 , HOH D:761BINDING SITE FOR RESIDUE ZN C 501
09AC9SOFTWAREASP C:108 , GLU C:214 , HOH C:701 , HOH C:717BINDING SITE FOR RESIDUE ZN C 503
10BC1SOFTWAREASP B:97 , HOH B:696 , GLU C:146 , HOH C:657BINDING SITE FOR RESIDUE ZN C 504
11BC2SOFTWAREEDO C:13 , GLU C:169 , HOH C:557 , HOH C:566 , HIS D:77BINDING SITE FOR RESIDUE ZN C 505
12BC3SOFTWAREGLN C:79 , PRO C:80 , ASP C:81 , SER C:82 , HOH C:564 , HOH C:597BINDING SITE FOR RESIDUE ACT C 4
13BC4SOFTWAREGLU C:138 , GLU D:138 , HOH D:823 , HOH D:887 , HOH D:946BINDING SITE FOR RESIDUE ZN D 502
14BC5SOFTWARETHR C:45 , ASN C:63 , THR D:45 , ASN D:63 , ARG D:66 , HOH D:741 , HOH D:753 , HOH D:859 , HOH D:866BINDING SITE FOR RESIDUE ACT D 2
15BC6SOFTWAREGLN D:79 , PRO D:80 , ASP D:81 , SER D:82 , HOH D:842 , HOH D:909BINDING SITE FOR RESIDUE ACT D 5
16BC7SOFTWARETYR A:172 , GLU A:206 , ILE A:209 , VAL A:211 , HOH A:516 , HOH A:610BINDING SITE FOR RESIDUE EDO A 6
17BC8SOFTWAREALA A:96 , SER A:100 , TRP A:101 , HOH A:520 , HOH A:673 , HOH A:697BINDING SITE FOR RESIDUE EDO A 12
18BC9SOFTWAREGLN A:178 , LYS A:181 , ALA A:182 , GLN A:185 , HOH A:505 , HOH A:777 , ASP D:130BINDING SITE FOR RESIDUE EDO A 18
19CC1SOFTWAREALA A:149 , GLY A:151 , ACT B:1 , GLY B:78 , PRO B:80 , ASP B:81 , HOH B:599 , HOH B:712BINDING SITE FOR RESIDUE EDO A 19
20CC2SOFTWAREALA A:62 , ILE A:121 , ASN A:122 , HOH A:510 , HOH A:523 , HOH A:718BINDING SITE FOR RESIDUE EDO A 25
21CC3SOFTWAREASN B:122 , HOH B:518 , HOH B:521 , HOH B:677BINDING SITE FOR RESIDUE EDO B 14
22CC4SOFTWAREALA B:96 , SER B:100 , TRP B:101 , HOH B:514 , HOH B:637 , HOH B:723BINDING SITE FOR RESIDUE EDO B 15
23CC5SOFTWAREEDO B:22 , MSE B:215 , ALA C:109BINDING SITE FOR RESIDUE EDO B 21
24CC6SOFTWAREEDO B:21 , ARG B:161 , LYS C:85 , HOH C:563BINDING SITE FOR RESIDUE EDO B 22
25CC7SOFTWAREGLN A:69 , TYR B:172 , HOH B:730 , HOH B:798BINDING SITE FOR RESIDUE EDO B 24
26CC8SOFTWARESER A:124 , HOH A:708 , HOH B:750 , HOH B:781BINDING SITE FOR RESIDUE EDO B 27
27CC9SOFTWAREGLU B:206 , ILE B:209 , VAL B:211 , HOH B:534 , HOH B:722BINDING SITE FOR RESIDUE EDO B 29
28DC1SOFTWAREILE C:121 , ASN C:122 , HOH C:522 , HOH C:527 , HOH C:697BINDING SITE FOR RESIDUE EDO C 7
29DC2SOFTWARELYS C:49 , GLN C:60 , ALA C:96 , SER C:100 , TRP C:101 , HOH C:521 , HOH C:587BINDING SITE FOR RESIDUE EDO C 11
30DC3SOFTWARELEU C:55 , VAL C:57 , GLU C:169 , GLN C:171 , ZN C:505 , HOH C:557 , HOH C:566 , HOH C:721 , HIS D:77BINDING SITE FOR RESIDUE EDO C 13
31DC4SOFTWAREASP B:130 , LYS C:181 , ALA C:182 , GLN C:185 , HOH C:518BINDING SITE FOR RESIDUE EDO C 20
32DC5SOFTWAREHOH D:717 , HOH D:947BINDING SITE FOR RESIDUE EDO D 8
33DC6SOFTWARELYS D:49 , ALA D:96 , SER D:100 , TRP D:101 , HOH D:724 , HOH D:853 , HOH D:855BINDING SITE FOR RESIDUE EDO D 9
34DC7SOFTWAREALA A:115 , HOH A:598 , GLN B:46 , GLU B:50 , HOH B:659 , ARG D:161BINDING SITE FOR RESIDUE EDO D 10
35DC8SOFTWAREHIS C:77 , ZN C:501 , LEU D:55 , VAL D:57 , GLU D:169 , HOH D:730 , HOH D:761BINDING SITE FOR RESIDUE EDO D 16
36DC9SOFTWAREASP A:130 , GLN D:178 , ALA D:182 , GLN D:185 , HOH D:731BINDING SITE FOR RESIDUE EDO D 17
37EC1SOFTWAREGLN C:69 , TYR D:172 , HOH D:958BINDING SITE FOR RESIDUE EDO D 23
38EC2SOFTWAREILE D:121 , ASN D:122 , HOH D:725 , HOH D:733 , HOH D:906BINDING SITE FOR RESIDUE EDO D 26
39EC3SOFTWAREARG A:161 , MSE A:215BINDING SITE FOR RESIDUE EDO D 28

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3DZA)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3DZA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3DZA)

(-) Sequences/Alignments

Asymmetric/Biological 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:180
 aligned with A6TE93_KLEP7 | A6TE93 from UniProtKB/TrEMBL  Length:220

    Alignment length:180
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217
         A6TE93_KLEP7    38 APAAAATTQVQKEAADVLQVAVQGANAMRDIQFARLALFHGQPDSAKKLTDDAAALLAADDASWAKFVKTDAKAKMIADRYVIINASIALSEDYVATPEKESAIQSANEKLAKGDQKGAIDTLRLAGIGVIENQYLMPLNQTRKAVAQSQELLKAGKYYEANLVLKGAEEGIVVDSEMLV 217
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.hhhhhhh..............eeeeeeeeeee.....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhh..eeeeeeeeeehhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3dza A  38 APAAAATTQVQKEAADVLQVAVQGANAmRDIQFARLALFHGQPDSAKKLTDDAAALLAADDASWAKFVKTDAKAKmIADRYVIINASIALSEDYVATPEKESAIQSANEKLAKGDQKGAIDTLRLAGIGVIENQYLmPLNQTRKAVAQSQELLKAGKYYEANLVLKGAEEGIVVDSEmLV 217
                                    47        57       |67        77        87        97       107     | 117       127       137       147       157       167      |177       187       197       207       217
                                                      65-MSE                                         113-MSE                                                      174-MSE                                  215-MSE


Chain B from PDB  Type:PROTEIN  Length:180
 aligned with A6TE93_KLEP7 | A6TE93 from UniProtKB/TrEMBL  Length:220

    Alignment length:180
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217
         A6TE93_KLEP7    38 APAAAATTQVQKEAADVLQVAVQGANAMRDIQFARLALFHGQPDSAKKLTDDAAALLAADDASWAKFVKTDAKAKMIADRYVIINASIALSEDYVATPEKESAIQSANEKLAKGDQKGAIDTLRLAGIGVIENQYLMPLNQTRKAVAQSQELLKAGKYYEANLVLKGAEEGIVVDSEMLV 217
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.hhhhhhhhh............eeeeeeeeeee.....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhh..eeeeeeeeeehhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3dza B  38 APAAAATTQVQKEAADVLQVAVQGANAmRDIQFARLALFHGQPDSAKKLTDDAAALLAADDASWAKFVKTDAKAKmIADRYVIINASIALSEDYVATPEKESAIQSANEKLAKGDQKGAIDTLRLAGIGVIENQYLmPLNQTRKAVAQSQELLKAGKYYEANLVLKGAEEGIVVDSEmLV 217
                                    47        57       |67        77        87        97       107     | 117       127       137       147       157       167      |177       187       197       207       217
                                                      65-MSE                                         113-MSE                                                      174-MSE                                  215-MSE


Chain C from PDB  Type:PROTEIN  Length:175
 aligned with A6TE93_KLEP7 | A6TE93 from UniProtKB/TrEMBL  Length:220

    Alignment length:175
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212     
         A6TE93_KLEP7    43 ATTQVQKEAADVLQVAVQGANAMRDIQFARLALFHGQPDSAKKLTDDAAALLAADDASWAKFVKTDAKAKMIADRYVIINASIALSEDYVATPEKESAIQSANEKLAKGDQKGAIDTLRLAGIGVIENQYLMPLNQTRKAVAQSQELLKAGKYYEANLVLKGAEEGIVVDSEMLV 217
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhh..............eeeeeeeeeee.....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhh..eeeeeeeeeehhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dza C  43 ATTQVQKEAADVLQVAVQGANAmRDIQFARLALFHGQPDSAKKLTDDAAALLAADDASWAKFVKTDAKAKmIADRYVIINASIALSEDYVATPEKESAIQSANEKLAKGDQKGAIDTLRLAGIGVIENQYLmPLNQTRKAVAQSQELLKAGKYYEANLVLKGAEEGIVVDSEmLV 217
                                    52        62  |     72        82        92       102       112|      122       132       142       152       162       172 |     182       192       202       212  |  
                                                 65-MSE                                         113-MSE                                                      174-MSE                                  215-MSE


Chain D from PDB  Type:PROTEIN  Length:176
 aligned with A6TE93_KLEP7 | A6TE93 from UniProtKB/TrEMBL  Length:220

    Alignment length:176
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211      
         A6TE93_KLEP7    42 AATTQVQKEAADVLQVAVQGANAMRDIQFARLALFHGQPDSAKKLTDDAAALLAADDASWAKFVKTDAKAKMIADRYVIINASIALSEDYVATPEKESAIQSANEKLAKGDQKGAIDTLRLAGIGVIENQYLMPLNQTRKAVAQSQELLKAGKYYEANLVLKGAEEGIVVDSEMLV 217
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhh............eeeeeeeeeee.....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhh..eeeeeeeeeehhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.eeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dza D  42 AATTQVQKEAADVLQVAVQGANAmRDIQFARLALFHGQPDSAKKLTDDAAALLAADDASWAKFVKTDAKAKmIADRYVIINASIALSEDYVATPEKESAIQSANEKLAKGDQKGAIDTLRLAGIGVIENQYLmPLNQTRKAVAQSQELLKAGKYYEANLVLKGAEEGIVVDSEmLV 217
                                    51        61   |    71        81        91       101       111 |     121       131       141       151       161       171  |    181       191       201       211   |  
                                                  65-MSE                                         113-MSE                                                      174-MSE                                  215-MSE
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3DZA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (A6TE93_KLEP7 | A6TE93)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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