Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  TRANSITION-STATE MIMICRY IN MANNOSIDE HYDROLYSIS: CHARACTERISATION OF TWENTY SIX INHIBITORS AND INSIGHT INTO BINDING FROM LINEAR FREE ENERGY RELATIONSHIPS AND 3-D STRUCTURE
 
Authors :  L. E. Tailford, W. A. Offen, N. L. Smith, C. Dumon, C. Moreland, J. Gratien, M. P. Heck, R. V. Stick, Y. Bleriot, A. Vasella, H. J. Gilbert, G. J. Davies
Date :  25 Mar 08  (Deposition) - 08 Apr 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Linear Free Energy Relationship, Hydrolase, Transition State Mimic, Mannosidase, Glycoside Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. E. Tailford, W. A. Offen, N. L. Smith, C. Dumon, C. Morland, J. Gratien, M. P. Heck, R. V. Stick, Y. Bleriot, A. Vasella, H. J. Gilbert, G. J. Davies
Structural And Biochemical Evidence For A Boat-Like Transition State In Beta-Mannosidases.
Nat. Chem. Biol. V. 4 306 2008
PubMed-ID: 18408714  |  Reference-DOI: 10.1038/NCHEMBIO.81

(-) Compounds

Molecule 1 - BETA-MANNOSIDASE
    Atcc: 29148
    Chains: A, B
    EC Number: 3.2.1.25
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Fragment: RESIDUES 26-864
    Organism Scientific: BACTEROIDES THETAIOTAOMICRON
    Organism Taxid: 226186
    Strain: VPI-5482

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 71)

Asymmetric Unit (4, 71)
No.NameCountTypeFull Name
117B2Ligand/Ion(2Z,3R,4S,5R,6R)-2-[(4-AMINOBUTYL)IMINO]-6-(HYDROXYMETHYL)PIPERIDINE-3,4,5-TRIOL
2BR8Ligand/IonBROMIDE ION
3CL11Ligand/IonCHLORIDE ION
4EDO50Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (2, 22)
No.NameCountTypeFull Name
117B1Ligand/Ion(2Z,3R,4S,5R,6R)-2-[(4-AMINOBUTYL)IMINO]-6-(HYDROXYMETHYL)PIPERIDINE-3,4,5-TRIOL
2BR-1Ligand/IonBROMIDE ION
3CL-1Ligand/IonCHLORIDE ION
4EDO21Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (2, 30)
No.NameCountTypeFull Name
117B1Ligand/Ion(2Z,3R,4S,5R,6R)-2-[(4-AMINOBUTYL)IMINO]-6-(HYDROXYMETHYL)PIPERIDINE-3,4,5-TRIOL
2BR-1Ligand/IonBROMIDE ION
3CL-1Ligand/IonCHLORIDE ION
4EDO29Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (70, 70)

Asymmetric Unit (70, 70)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG B:597 , PRO B:607 , GLU B:608 , SER B:609 , PHE B:610 , PHE B:613 , HOH B:2408BINDING SITE FOR RESIDUE EDO A1886
02AC2SOFTWAREASN A:518 , TRP A:519 , GLY A:520 , HOH A:2567 , HOH A:2568BINDING SITE FOR RESIDUE EDO A1888
03AC3SOFTWAREILE B:282 , HIS B:284BINDING SITE FOR RESIDUE EDO B1903
04AC4SOFTWAREGLU A:243 , LEU A:244 , ILE A:245 , HIS A:284 , ILE A:285 , THR A:286 , HOH A:2569BINDING SITE FOR RESIDUE EDO A1893
05AC5SOFTWAREPHE A:775 , ARG A:777 , LYS A:778 , EDO A:1872 , CL A:1887BINDING SITE FOR RESIDUE EDO A1894
06AC6SOFTWAREASP A:603 , LYS A:778 , THR A:779 , HOH A:2418BINDING SITE FOR RESIDUE CL A1897
07AC7SOFTWAREGLN A:768 , ALA A:770 , HOH A:2499BINDING SITE FOR RESIDUE CL B1901
08AC8SOFTWARETRP B:198 , ASP B:199 , TRP B:200 , TRP B:395 , ASN B:461 , GLU B:462 , TRP B:533 , TYR B:537 , GLU B:555 , TRP B:645 , TRP B:656 , HOH B:2557BINDING SITE FOR RESIDUE 17B B1869
09AC9SOFTWARETRP A:198 , ASP A:199 , TRP A:200 , TRP A:395 , ASN A:461 , GLU A:462 , TRP A:533 , TYR A:537 , GLU A:555 , TRP A:645 , TRP A:656 , HOH A:2553 , HOH A:2554BINDING SITE FOR RESIDUE 17B A1865
10BC1SOFTWAREILE A:684 , GLN A:685 , EDO A:1894 , HOH A:2464BINDING SITE FOR RESIDUE CL A1887
11BC2SOFTWAREGLN A:365 , ASN A:648 , ASP A:649 , ILE A:659 , ASP A:660BINDING SITE FOR RESIDUE EDO A1866
12BC3SOFTWAREARG A:211 , PRO A:212 , ASN A:402 , HOH A:2136 , HOH A:2290BINDING SITE FOR RESIDUE EDO A1889
13BC4SOFTWARETRP B:525 , SER B:530 , ASN B:532 , ASP B:548 , LEU B:549 , PRO B:550 , MET B:553 , HOH B:2558BINDING SITE FOR RESIDUE EDO B1870
14BC5SOFTWARETRP A:525 , SER A:530 , ASN A:532 , ASP A:548 , PRO A:550 , MET A:553 , HOH A:2555BINDING SITE FOR RESIDUE EDO A1867
15BC6SOFTWAREILE A:328 , GLY A:329 , ARG A:449 , ASN A:450 , HIS A:451 , ALA A:452 , ARG A:507 , HOH A:2154BINDING SITE FOR RESIDUE EDO A1868
16BC7SOFTWAREARG A:331 , ARG A:507 , HOH A:2556 , HOH A:2557 , HOH A:2558BINDING SITE FOR RESIDUE EDO A1869
17BC8SOFTWAREILE A:578 , ARG A:597 , PRO A:607 , GLU A:608 , SER A:609 , PHE A:613 , HOH A:2559 , HOH A:2560BINDING SITE FOR RESIDUE EDO A1870
18BC9SOFTWAREASN A:337 , HIS A:511 , TYR A:515 , HOH A:2254 , HOH A:2561BINDING SITE FOR RESIDUE EDO A1871
19CC1SOFTWAREASN B:337 , HIS B:511 , TYR B:515 , HOH B:2559 , HOH B:2560 , HOH B:2561BINDING SITE FOR RESIDUE EDO B1871
20CC2SOFTWAREGLN A:623 , ARG A:626 , HIS A:774 , PHE A:775 , EDO A:1894 , HOH A:2562 , HOH A:2563BINDING SITE FOR RESIDUE EDO A1872
21CC3SOFTWARETHR A:432 , HOH A:2064 , LEU B:126BINDING SITE FOR RESIDUE EDO B1872
22CC4SOFTWARESER B:43 , GLN B:44 , SER B:45 , GLY B:46 , THR B:47 , GLU B:48 , GLU B:90BINDING SITE FOR RESIDUE EDO B1873
23CC5SOFTWARESER A:825 , ILE A:840 , THR A:842 , HOH A:2278BINDING SITE FOR RESIDUE EDO A1873
24CC6SOFTWAREARG B:331 , ASP B:506 , ARG B:507 , EDO B:1889 , HOH B:2246 , HOH B:2562 , HOH B:2563BINDING SITE FOR RESIDUE EDO B1874
25CC7SOFTWAREGLN B:365 , ASN B:648 , ASP B:649 , ILE B:659 , ASP B:660BINDING SITE FOR RESIDUE EDO B1875
26CC8SOFTWAREGLU B:465 , LYS B:468 , TYR B:469 , PRO B:514 , LEU B:516 , ALA B:517 , ASN B:518BINDING SITE FOR RESIDUE EDO B1876
27CC9SOFTWAREHIS A:326 , ARG A:327 , ASN A:450 , HIS A:451 , HOH A:2320 , HOH A:2564BINDING SITE FOR RESIDUE EDO A1874
28DC1SOFTWAREPHE B:356 , ARG B:633 , ARG B:636 , ILE B:695 , SER B:696 , ASP B:697 , ASN B:733 , THR B:734BINDING SITE FOR RESIDUE EDO B1877
29DC2SOFTWAREILE B:328 , GLY B:329 , ARG B:449 , ASN B:450 , HIS B:451 , ALA B:452 , ARG B:507 , HOH B:2178BINDING SITE FOR RESIDUE EDO B1878
30DC3SOFTWAREPHE A:42 , SER A:43 , LYS A:49 , MET A:51BINDING SITE FOR RESIDUE EDO A1875
31DC4SOFTWAREPHE B:775 , ARG B:777 , LYS B:778 , EDO B:1899BINDING SITE FOR RESIDUE EDO B1879
32DC5SOFTWARESER B:43 , GLN B:44 , THR B:47 , LYS B:49 , HOH B:2012BINDING SITE FOR RESIDUE EDO B1880
33DC6SOFTWAREARG B:382 , ARG B:823 , SER B:825 , ILE B:840 , THR B:842 , HOH B:2579BINDING SITE FOR RESIDUE EDO B1881
34DC7SOFTWAREHIS B:326 , ARG B:327 , ASN B:450 , HIS B:451 , HOH B:2241 , HOH B:2333 , HOH B:2564BINDING SITE FOR RESIDUE EDO B1882
35DC8SOFTWAREARG B:447BINDING SITE FOR RESIDUE CL B1902
36DC9SOFTWAREGLN B:108BINDING SITE FOR RESIDUE CL B1883
37EC1SOFTWARETRP A:536 , TYR A:537 , SER A:589 , SER A:590 , ILE A:591BINDING SITE FOR RESIDUE CL A1890
38EC2SOFTWAREHOH B:2350 , HOH B:2559BINDING SITE FOR RESIDUE CL B1904
39EC3SOFTWAREILE A:107 , LYS A:142BINDING SITE FOR RESIDUE BR A1877
40EC4SOFTWAREHIS A:284BINDING SITE FOR RESIDUE BR A1878
41EC5SOFTWAREGLN B:685 , ASP B:688BINDING SITE FOR RESIDUE BR B1884
42EC6SOFTWAREILE B:107 , LYS B:142 , HOH B:2103BINDING SITE FOR RESIDUE BR B1885
43EC7SOFTWAREPHE A:476 , THR A:477BINDING SITE FOR RESIDUE CL A1880
44EC8SOFTWAREASN A:337BINDING SITE FOR RESIDUE CL A1892
45EC9SOFTWAREGLU B:112 , THR B:214 , ARG B:216 , HOH B:2576BINDING SITE FOR RESIDUE EDO B1905
46FC1SOFTWARELEU B:35 , LEU B:36 , ASP B:37 , THR B:38 , SER B:94 , PHE B:95BINDING SITE FOR RESIDUE EDO B1906
47FC2SOFTWAREASP B:688 , ASP B:744 , LEU B:747 , PRO B:749 , ARG B:777BINDING SITE FOR RESIDUE EDO B1886
48FC3SOFTWARETYR B:347 , HOH B:2252 , HOH B:2565 , HOH B:2566BINDING SITE FOR RESIDUE EDO B1887
49FC4SOFTWAREGLN A:108BINDING SITE FOR RESIDUE BR A1891
50FC5SOFTWAREGLN B:230 , THR B:332 , ASP B:506 , EDO B:1874 , HOH B:2569BINDING SITE FOR RESIDUE EDO B1889
51FC6SOFTWAREASN B:300 , ASN B:390 , HOH B:2268BINDING SITE FOR RESIDUE CL B1891
52FC7SOFTWAREARG B:376 , TYR B:661 , TYR B:662BINDING SITE FOR RESIDUE EDO B1892
53FC8SOFTWAREGLN B:795 , ARG B:845 , ILE B:846 , LYS B:847 , GLU B:850BINDING SITE FOR RESIDUE EDO B1907
54FC9SOFTWAREMET B:298 , TRP B:302 , ASN B:351BINDING SITE FOR RESIDUE CL B1894
55GC1SOFTWAREARG A:633 , ARG A:636 , ILE A:695 , SER A:696 , ASP A:697 , ASN A:733 , THR A:734BINDING SITE FOR RESIDUE EDO A1881
56GC2SOFTWAREGLY B:538 , LYS B:539 , LYS B:540 , PRO B:541 , EDO B:1898 , HOH B:2577BINDING SITE FOR RESIDUE EDO B1908
57GC3SOFTWAREASN A:300 , ASN A:390 , HOH A:2258 , HOH A:2259BINDING SITE FOR RESIDUE BR A1882
58GC4SOFTWAREMET A:76 , LYS A:79BINDING SITE FOR RESIDUE EDO A1895
59GC5SOFTWARETYR A:347 , HOH A:2248 , HOH A:2565 , HOH A:2566BINDING SITE FOR RESIDUE EDO A1883
60GC6SOFTWARESER A:765 , HIS A:767 , HOH A:2570 , SER B:98 , GLU B:100 , GLN B:101BINDING SITE FOR RESIDUE EDO A1896
61GC7SOFTWARETYR B:443 , ARG B:446 , HOH B:2169 , HOH B:2328 , HOH B:2570BINDING SITE FOR RESIDUE EDO B1896
62GC8SOFTWAREVAL B:372 , THR B:374 , TYR B:377 , ASN B:402 , LEU B:404 , HOH B:2571BINDING SITE FOR RESIDUE EDO B1897
63GC9SOFTWAREGLU B:243 , LEU B:244 , ILE B:245 , HIS B:284 , ILE B:285 , THR B:286 , HOH B:2578BINDING SITE FOR RESIDUE EDO B1909
64HC1SOFTWAREPRO B:541 , ARG B:602 , EDO B:1908 , HOH B:2573BINDING SITE FOR RESIDUE EDO B1898
65HC2SOFTWAREGLU A:494 , PRO A:497 , SER A:498BINDING SITE FOR RESIDUE EDO A1898
66HC3SOFTWAREGLN A:685 , ASP A:688BINDING SITE FOR RESIDUE BR A1884
67HC4SOFTWAREVAL A:442 , ARG A:446 , HOH A:2071 , HOH A:2312BINDING SITE FOR RESIDUE EDO A1885
68HC5SOFTWAREGLN B:623 , ARG B:626 , PHE B:775 , EDO B:1879 , HOH B:2438 , HOH B:2523 , HOH B:2574BINDING SITE FOR RESIDUE EDO B1899
69HC6SOFTWARETRP B:665 , TYR B:670 , ARG B:823 , TYR B:824 , HOH B:2459 , HOH B:2579BINDING SITE FOR RESIDUE EDO B1910
70HC7SOFTWAREASP A:119 , LYS A:129 , HIS A:157 , GLN A:162 , ASP B:119 , LYS B:129 , HIS B:157 , GLN B:162 , HOH B:2071 , HOH B:2575BINDING SITE FOR RESIDUE EDO B1900

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VR4)

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Val A:55 -Pro A:56
2Asp A:115 -Thr A:116
3Ser A:513 -Pro A:514
4Arg A:636 -Pro A:637
5Trp A:645 -Gln A:646
6Val B:55 -Pro B:56
7Asp B:115 -Thr B:116
8Ser B:513 -Pro B:514
9Arg B:636 -Pro B:637
10Trp B:645 -Gln B:646

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VR4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VR4)

(-) Exons   (0, 0)

(no "Exon" information available for 2VR4)

(-) 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:836
 aligned with Q8AAK6_BACTN | Q8AAK6 from UniProtKB/TrEMBL  Length:864

    Alignment length:837
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       
         Q8AAK6_BACTN    28 NDTSEVMLLDTGWEFSQSGTEKWMPATVPGTVHQDLISHELLPNPFYGMNEKKIQWVENEDWEYRTSFIVSEEQLNRDGIQLIFEGLDTYADVYLNGSLLLKADNMFVGYTLPVKSVLRKGENHLYIYFHSPIRQTLPQYASNGFNYPADNDHHEKHLSVFSRKAPYSYGWDWGIRMVTSGVWRPVTLRFYDIATISDYYVRQLSLTDENARLSNELIVNQIVPQKIPAEVRVNVSLNGTTVTEVKQQVTLQPGINHITLPAEVTNPVRWMPNGWGTPTLYDFSAQIACGDRIVAEQSHRIGLRTIRVVNEKDKDGESFYFEVNGIPMFAKGANYIPQDALLPNVTTERYQTLFRDMKEANMNMVRIWGGGTYENNLFYDLADENGILVWQDFMFACTPYPSDPTFLKRVEAEAVYNIRRLRNHASLAMWCGNNEILEALKYWGFEKKFTPEVYQGLMHGYDKLFRELLPSTVKEFDSDRFYVHSSPYLANWGRPESWGTGDSHNWGVWYGKKPFESLDTDLPRFMSEFGFQSFPEMKTIAAFAAPEDYQIESEVMNAHQKSSIGNSLIRTYMERDYIIPESFEDFVYVGLVLQGQGMRHGLEAHRRNRPYCMGTLYWQLNDSWPVVSWSSIDYYGNWKALHYQAKRAFAPVLINPIQQNDSLSVYLISDRLDTMEQMTLEMKVVDFDGKTLGKKIQVHSLEVPANTSKCVYRAKLDGWLTPEDCRRSFLKLILKDKSGHQVAESVHFFRKTKDLQLPPTSVSYQMKQTDGKCELTLFSSMLAKDIFIETPLQGARYSDNFFDLLPGERKKVIITSPRIKKGEELPVNIKHIRETYK 864
               SCOP domains d2vr4a4 A:28-219 automated matches                                                                                                                                                              d2vr4a1 A:220-330 automated matches                                                                            d2vr4a5 A:331-678 automated matches                                                                                                                                                                                                                                                                                                                         d2vr4a3 A:679-783 automated matches                                                                      d2vr4a2 A:784-864 automated matches                                               SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee.....eeee......ee.....hhhhhhhh............hhhhhhhhhh.eeeeeeeeehhhhhh..eeeeee..ee.eeeeee..eeeeeee.....eeee.hhhh..eeeeeeeeeehhhhhhhhhhhhhh............hhhhhh..hhhhhh..........ee...eeeeee..eeeeeeeeeeeee...eeeeeeeeeeee.....eeeeeeeeeee..eeeeeeeeeeee..eeeeeeeeeeee...............eeeeeeeee..eeeeeeeeee....eeee..ee..ee..eeee..eee.eeeeee.....hhhhhhhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhh.eeeee..........hhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee..........hhhhh....ee.........hhhhhhh.....eee.......hhhhhhhhhhhhhh....hhhhhh.....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee.....................hhhhhhhhhhh..eeeeeeee..eeeeeeee.....eeeeeeeeeeee....eeeeeeeeeeeee...eeeeeeeee.....hhhhhh.eeeeeeee.....eeeeeeee..hhhhh.......eeeeeee..eeeeeee....eeeeeee......ee....eee.....eeeeee.......-....eeehhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vr4 A  28 NDTSEVMLLDTGWEFSQSGTEKWMPATVPGTVHQDLISHELLPNPFYGMNEKKIQWVENEDWEYRTSFIVSEEQLNRDGIQLIFEGLDTYADVYLNGSLLLKADNMFVGYTLPVKSVLRKGENHLYIYFHSPIRQTLPQYASNGFNYPADNDHHEKHLSVFSRKAPYSYGWDWGIRMVTSGVWRPVTLRFYDIATISDYYVRQLSLTDENARLSNELIVNQIVPQKIPAEVRVNVSLNGTTVTEVKQQVTLQPGINHITLPAEVTNPVRWMPNGWGTPTLYDFSAQIACGDRIVAEQSHRIGLRTIRVVNEKDKDGESFYFEVNGIPMFAKGANYIPQDALLPNVTTERYQTLFRDMKEANMNMVRIWGGGTYENNLFYDLADENGILVWQDFMFACTPYPSDPTFLKRVEAEAVYNIRRLRNHASLAMWCGNNEILEALKYWGFEKKFTPEVYQGLMHGYDKLFRELLPSTVKEFDSDRFYVHSSPYLANWGRPESWGTGDSHNWGVWYGKKPFESLDTDLPRFMSEFGFQSFPEMKTIAAFAAPEDYQIESEVMNAHQKSSIGNSLIRTYMERDYIIPESFEDFVYVGLVLQGQGMRHGLEAHRRNRPYCMGTLYWQLNDSWPVVSWSSIDYYGNWKALHYQAKRAFAPVLINPIQQNDSLSVYLISDRLDTMEQMTLEMKVVDFDGKTLGKKIQVHSLEVPANTSKCVYRAKLDGWLTPEDCRRSFLKLILKDKSGHQVAESVHFFRKTKDLQLPPTSVSYQMKQTDGKCELTLFSSMLAKDIFIETPLQGARYSDNFFDLLPGERKKVIITSPRIKKG-ELPVNIKHIRETYK 864
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847 | |   857       
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               849 |             
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 851             


Chain B from PDB  Type:PROTEIN  Length:841
 aligned with Q8AAK6_BACTN | Q8AAK6 from UniProtKB/TrEMBL  Length:864

    Alignment length:841
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               864   
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       | - 
         Q8AAK6_BACTN    27 GNDTSEVMLLDTGWEFSQSGTEKWMPATVPGTVHQDLISHELLPNPFYGMNEKKIQWVENEDWEYRTSFIVSEEQLNRDGIQLIFEGLDTYADVYLNGSLLLKADNMFVGYTLPVKSVLRKGENHLYIYFHSPIRQTLPQYASNGFNYPADNDHHEKHLSVFSRKAPYSYGWDWGIRMVTSGVWRPVTLRFYDIATISDYYVRQLSLTDENARLSNELIVNQIVPQKIPAEVRVNVSLNGTTVTEVKQQVTLQPGINHITLPAEVTNPVRWMPNGWGTPTLYDFSAQIACGDRIVAEQSHRIGLRTIRVVNEKDKDGESFYFEVNGIPMFAKGANYIPQDALLPNVTTERYQTLFRDMKEANMNMVRIWGGGTYENNLFYDLADENGILVWQDFMFACTPYPSDPTFLKRVEAEAVYNIRRLRNHASLAMWCGNNEILEALKYWGFEKKFTPEVYQGLMHGYDKLFRELLPSTVKEFDSDRFYVHSSPYLANWGRPESWGTGDSHNWGVWYGKKPFESLDTDLPRFMSEFGFQSFPEMKTIAAFAAPEDYQIESEVMNAHQKSSIGNSLIRTYMERDYIIPESFEDFVYVGLVLQGQGMRHGLEAHRRNRPYCMGTLYWQLNDSWPVVSWSSIDYYGNWKALHYQAKRAFAPVLINPIQQNDSLSVYLISDRLDTMEQMTLEMKVVDFDGKTLGKKIQVHSLEVPANTSKCVYRAKLDGWLTPEDCRRSFLKLILKDKSGHQVAESVHFFRKTKDLQLPPTSVSYQMKQTDGKCELTLFSSMLAKDIFIETPLQGARYSDNFFDLLPGERKKVIITSPRIKKGEELPVNIKHIRETYK---   -
               SCOP domains d2vr4b4 B:27-219 automated matches                                                                                                                                                               d2vr4b1 B:220-330 automated matches                                                                            d2vr4b5 B:331-678 automated matches                                                                                                                                                                                                                                                                                                                         d2vr4b3 B:679-783 automated matches                                                                      d2vr4b2 B:784-867 automated matches                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -Glyco_hydro_2_N-2vr4B01 B:28-219                                                                                                                                                                -Glyco_hydro_2-2vr4B05 B:221-331                                                                                -------------Glyco_hydro_2_C-2vr4B03 B:345-478                                                                                                     ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -Glyco_hydro_2_N-2vr4B02 B:28-219                                                                                                                                                                -Glyco_hydro_2-2vr4B06 B:221-331                                                                                -------------Glyco_hydro_2_C-2vr4B04 B:345-478                                                                                                     ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .....eeee.....eeee......ee.....hhhhhhhhh...........hhhhhhhhhh.eeeeeeeeehhhhhh..eeeeee..ee.eeeeee..eeeeeee.....eeee.hhhh..eeeeeeeeeehhhhhhhhhhhhhh............hhhhhh..hhhhhh..........ee...eeeeee..eeeeeeeeeeeee...eeeeeeeeeeee.....eeeeeeeeeee..eeeeeeeeeeee..eeeeeeeeeeee...............eeeeeeeee..eeeeeeeeee....eeee..ee..ee..eeee..eee.eeeeee.....hhhhhhhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhh.eeeee..........hhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee..........hhhhh...eee.........hhhhhhh....eeee.......hhhhhhhhhhhhhh...hhhhhhh....hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee.....................hhhhhhhhhhh..eeeeeeee..eeeeeeee.....eeeeeeeeeeee....eeeeeeeeeeeee...eeeeeeeee.....hhhhhh.eeeeeeee.....eeeeeeee..hhhhh.......eeeeeee..eeeeeee....eeeeeee......ee....eee.....eeeeee............eeehhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vr4 B  27 GNDTSEVMLLDTGWEFSQSGTEKWMPATVPGTVHQDLISHELLPNPFYGMNEKKIQWVENEDWEYRTSFIVSEEQLNRDGIQLIFEGLDTYADVYLNGSLLLKADNMFVGYTLPVKSVLRKGENHLYIYFHSPIRQTLPQYASNGFNYPADNDHHEKHLSVFSRKAPYSYGWDWGIRMVTSGVWRPVTLRFYDIATISDYYVRQLSLTDENARLSNELIVNQIVPQKIPAEVRVNVSLNGTTVTEVKQQVTLQPGINHITLPAEVTNPVRWMPNGWGTPTLYDFSAQIACGDRIVAEQSHRIGLRTIRVVNEKDKDGESFYFEVNGIPMFAKGANYIPQDALLPNVTTERYQTLFRDMKEANMNMVRIWGGGTYENNLFYDLADENGILVWQDFMFACTPYPSDPTFLKRVEAEAVYNIRRLRNHASLAMWCGNNEILEALKYWGFEKKFTPEVYQGLMHGYDKLFRELLPSTVKEFDSDRFYVHSSPYLANWGRPESWGTGDSHNWGVWYGKKPFESLDTDLPRFMSEFGFQSFPEMKTIAAFAAPEDYQIESEVMNAHQKSSIGNSLIRTYMERDYIIPESFEDFVYVGLVLQGQGMRHGLEAHRRNRPYCMGTLYWQLNDSWPVVSWSSIDYYGNWKALHYQAKRAFAPVLINPIQQNDSLSVYLISDRLDTMEQMTLEMKVVDFDGKTLGKKIQVHSLEVPANTSKCVYRAKLDGWLTPEDCRRSFLKLILKDKSGHQVAESVHFFRKTKDLQLPPTSVSYQMKQTDGKCELTLFSSMLAKDIFIETPLQGARYSDNFFDLLPGERKKVIITSPRIKKGEELPVNIKHIRETYKEHH 867
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866
   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  (3, 10)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2VR4)

(-) Pfam Domains  (3, 6)

Asymmetric Unit
(-)
Clan: GBD (153)
(-)
Clan: Glyco_hydro_tim (488)
(-)
Clan: no clan defined [family: Glyco_hydro_2] (31)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8AAK6_BACTN | Q8AAK6)
molecular function
    GO:0004567    beta-mannosidase activity    Catalysis of the hydrolysis of terminal, non-reducing beta-D-mannose residues in beta-D-mannosides.
    GO:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
cellular component
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    17B  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    BR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
    CC1  [ RasMol ]  +environment [ RasMol ]
    CC2  [ RasMol ]  +environment [ RasMol ]
    CC3  [ RasMol ]  +environment [ RasMol ]
    CC4  [ RasMol ]  +environment [ RasMol ]
    CC5  [ RasMol ]  +environment [ RasMol ]
    CC6  [ RasMol ]  +environment [ RasMol ]
    CC7  [ RasMol ]  +environment [ RasMol ]
    CC8  [ RasMol ]  +environment [ RasMol ]
    CC9  [ RasMol ]  +environment [ RasMol ]
    DC1  [ RasMol ]  +environment [ RasMol ]
    DC2  [ RasMol ]  +environment [ RasMol ]
    DC3  [ RasMol ]  +environment [ RasMol ]
    DC4  [ RasMol ]  +environment [ RasMol ]
    DC5  [ RasMol ]  +environment [ RasMol ]
    DC6  [ RasMol ]  +environment [ RasMol ]
    DC7  [ RasMol ]  +environment [ RasMol ]
    DC8  [ RasMol ]  +environment [ RasMol ]
    DC9  [ RasMol ]  +environment [ RasMol ]
    EC1  [ RasMol ]  +environment [ RasMol ]
    EC2  [ RasMol ]  +environment [ RasMol ]
    EC3  [ RasMol ]  +environment [ RasMol ]
    EC4  [ RasMol ]  +environment [ RasMol ]
    EC5  [ RasMol ]  +environment [ RasMol ]
    EC6  [ RasMol ]  +environment [ RasMol ]
    EC7  [ RasMol ]  +environment [ RasMol ]
    EC8  [ RasMol ]  +environment [ RasMol ]
    EC9  [ RasMol ]  +environment [ RasMol ]
    FC1  [ RasMol ]  +environment [ RasMol ]
    FC2  [ RasMol ]  +environment [ RasMol ]
    FC3  [ RasMol ]  +environment [ RasMol ]
    FC4  [ RasMol ]  +environment [ RasMol ]
    FC5  [ RasMol ]  +environment [ RasMol ]
    FC6  [ RasMol ]  +environment [ RasMol ]
    FC7  [ RasMol ]  +environment [ RasMol ]
    FC8  [ RasMol ]  +environment [ RasMol ]
    FC9  [ RasMol ]  +environment [ RasMol ]
    GC1  [ RasMol ]  +environment [ RasMol ]
    GC2  [ RasMol ]  +environment [ RasMol ]
    GC3  [ RasMol ]  +environment [ RasMol ]
    GC4  [ RasMol ]  +environment [ RasMol ]
    GC5  [ RasMol ]  +environment [ RasMol ]
    GC6  [ RasMol ]  +environment [ RasMol ]
    GC7  [ RasMol ]  +environment [ RasMol ]
    GC8  [ RasMol ]  +environment [ RasMol ]
    GC9  [ RasMol ]  +environment [ RasMol ]
    HC1  [ RasMol ]  +environment [ RasMol ]
    HC2  [ RasMol ]  +environment [ RasMol ]
    HC3  [ RasMol ]  +environment [ RasMol ]
    HC4  [ RasMol ]  +environment [ RasMol ]
    HC5  [ RasMol ]  +environment [ RasMol ]
    HC6  [ RasMol ]  +environment [ RasMol ]
    HC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Arg A:636 - Pro A:637   [ RasMol ]  
    Arg B:636 - Pro B:637   [ RasMol ]  
    Asp A:115 - Thr A:116   [ RasMol ]  
    Asp B:115 - Thr B:116   [ RasMol ]  
    Ser A:513 - Pro A:514   [ RasMol ]  
    Ser B:513 - Pro B:514   [ RasMol ]  
    Trp A:645 - Gln A:646   [ RasMol ]  
    Trp B:645 - Gln B:646   [ RasMol ]  
    Val A:55 - Pro A:56   [ RasMol ]  
    Val B:55 - Pro B:56   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2vr4
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q8AAK6_BACTN | Q8AAK6
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  3.2.1.25
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q8AAK6_BACTN | Q8AAK6
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q8AAK6_BACTN | Q8AAK6: 2je8 2vjx 2vl4 2vmf 2vo5 2vot 2vqt 2vqu 2wbk

(-) Related Entries Specified in the PDB File

2je8 STRUCTURE OF A BETA-MANNOSIDASE FROM BACTEROIDES THETAIOTAOMICRON
2vjx STRUCTURAL AND BIOCHEMICAL EVIDENCE FOR A BOAT-LIKE TRANSITION STATE IN BETA- MANNOSIDASES
2vl4 STRUCTURAL AND BIOCHEMICAL EVIDENCE FOR A BOAT-LIKE TRANSITION STATE IN BETA- MANNOSIDASES
2vmf STRUCTURAL AND BIOCHEMICAL EVIDENCE FOR A BOAT-LIKE TRANSITION STATE IN BETA- MANNOSIDASES
2vo5 STRUCTURAL AND BIOCHEMICAL EVIDENCE FOR A BOAT-LIKE TRANSITION STATE IN BETA- MANNOSIDASES
2vot STRUCTURAL AND BIOCHEMICAL EVIDENCE FOR A BOAT-LIKE TRANSITION STATE IN BETA- MANNOSIDASES
2vqt STRUCTURAL AND BIOCHEMICAL EVIDENCE FOR A BOAT-LIKE TRANSITION STATE IN BETA- MANNOSIDASES
2vqu STRUCTURAL AND BIOCHEMICAL EVIDENCE FOR A BOAT-LIKE TRANSITION STATE IN BETA- MANNOSIDASES