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(-) Description

Title :  VARYING BINDING MODES OF INHIBITORS AND STRUCTURAL DIFFERENCES IN THE BINDING POCKETS OF DIFFERENT GAMMA-GLUTAMYLTRANSPEPTIDASES
 
Authors :  C. Bolz, N. C. Bach, H. Meyer, G. Mueller, M. Dawidowski, G. Popowicz, S. A. Skerra, M. Gerhard
Date :  28 May 15  (Deposition) - 18 May 16  (Release) - 18 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.49
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Gamma-Glutamyltranspeptidase, Ntn-Hydrolase, Acivicin, Proteros Biostructures Gmbh, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Bolz, N. C. Bach, H. Meyer, G. Mueller, M. Dawidowski, G. Popowicz, S. A. Sieber, A. Skerra, M. Gerhard
Varying Binding Modes Of Inhibitors And Structural Differences In The Binding Pockets Of Different Gamma-Glutamyltranspeptidases
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GAMMA-GLUTAMYLTRANSPEPTIDASE (GGT)
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: CATALYTIC DOMAIN, RESIDUES 1-379
    Gene: HP_1118
    Organism Scientific: HELICOBACTER PYLORI 26695
    Organism Taxid: 85962
 
Molecule 2 - GAMMA-GLUTAMYLTRANSPEPTIDASE (GGT)
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: CATALYTIC DOMAIN, RESIDUES 380-567
    Gene: HP_1118
    Organism Scientific: HELICOBACTER PYLORI 26695
    Organism Taxid: 85962
    Strain: / 26695

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 45)

Asymmetric Unit (2, 45)
No.NameCountTypeFull Name
14UD2Ligand/Ion(2S)-AMINO[(5S)-4,5-DIHYDRO-1,2-OXAZOL-5-YL]ACETIC ACID
2EDO43Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (2, 21)
No.NameCountTypeFull Name
14UD1Ligand/Ion(2S)-AMINO[(5S)-4,5-DIHYDRO-1,2-OXAZOL-5-YL]ACETIC ACID
2EDO20Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (2, 24)
No.NameCountTypeFull Name
14UD1Ligand/Ion(2S)-AMINO[(5S)-4,5-DIHYDRO-1,2-OXAZOL-5-YL]ACETIC ACID
2EDO23Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (45, 45)

Asymmetric Unit (45, 45)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:29 , HOH D:815binding site for residue EDO A 401
02AC2SOFTWAREHIS A:76 , HOH A:534 , HOH A:611 , LYS C:565 , HOH C:809binding site for residue EDO A 402
03AC3SOFTWARELEU A:180 , ARG A:184 , PHE A:197 , PHE A:198 , ASP A:204 , TYR A:205 , HOH A:647binding site for residue EDO A 403
04AC4SOFTWARESER A:28 , TYR A:29 , SER B:28 , TYR B:29 , SER C:499 , HOH C:802 , SER D:499 , HOH D:801binding site for residue EDO A 404
05AC5SOFTWAREASP A:341 , ASN A:345 , HOH A:694binding site for residue EDO A 405
06AC6SOFTWAREARG A:272 , GLY A:273 , TYR A:274 , LYS C:460 , ASN C:461binding site for residue EDO A 406
07AC7SOFTWAREGLU A:297 , HOH A:744binding site for residue EDO A 407
08AC8SOFTWAREASN A:94 , LEU A:188 , LYS A:189 , SER A:191 , LYS A:194binding site for residue EDO A 408
09AC9SOFTWAREALA A:145 , LYS A:148 , LYS A:149 , TRP A:263binding site for residue EDO A 409
10AD1SOFTWAREASN A:260 , HOH A:621 , LYS B:253 , ALA B:257binding site for residue EDO A 410
11AD2SOFTWAREARG A:103 , THR C:380 , THR C:398 , ASN C:400 , GLU C:419 , ASP C:422 , TYR C:433 , SER C:451 , SER C:452 , MET C:453 , GLY C:472 , GLY C:473 , ILE C:476 , HOH C:835binding site for residue 4UD C 701
12AD3SOFTWAREHIS A:91 , ALA A:93 , HOH A:511 , GLY C:390 , ASN C:462 , LYS C:463 , VAL C:464 , EDO C:707 , HOH C:816binding site for residue EDO C 702
13AD4SOFTWAREARG A:326 , ASP C:422 , PHE C:423 , SER C:424 , ASN C:429 , ASN C:431 , LEU C:435 , ASN C:441 , HOH C:849 , HOH C:868binding site for residue EDO C 703
14AD5SOFTWAREPRO C:501 , ARG C:502 , PHE C:503 , ILE C:514 , GLU C:515 , GLY C:518 , HOH C:807 , HOH C:875binding site for residue EDO C 704
15AD6SOFTWAREPRO A:30 , TYR B:29 , SER C:495 , SER C:560 , THR C:561 , HOH C:802 , HOH C:837binding site for residue EDO C 705
16AD7SOFTWAREALA A:93 , LYS A:194 , HIS A:202 , ASN C:391 , EDO C:711 , HOH C:820 , HOH C:867binding site for residue EDO C 706
17AD8SOFTWAREASP C:387 , GLY C:390 , SER C:555 , EDO C:702 , HOH C:839 , HOH C:861binding site for residue EDO C 707
18AD9SOFTWAREMET A:296 , ASN A:311 , SER C:485 , TYR C:490 , HOH C:823 , HOH C:836binding site for residue EDO C 708
19AE1SOFTWARELYS C:516 , PRO C:538 , VAL C:539 , HOH C:862 , HOH C:883binding site for residue EDO C 709
20AE2SOFTWAREASP C:522 , ASP C:525 , ASN C:526 , HOH C:817 , HOH C:841 , ASN D:526binding site for residue EDO C 710
21AE3SOFTWARETHR A:152 , GLY A:201 , HIS A:202 , TRP C:389 , EDO C:706 , HOH C:804 , HOH C:820binding site for residue EDO C 711
22AE4SOFTWAREGLU B:167 , LYS B:214 , HOH B:565binding site for residue EDO B 401
23AE5SOFTWARETHR B:152 , GLY B:201 , HIS B:202 , HOH B:574 , HOH B:711 , TRP D:389binding site for residue EDO B 402
24AE6SOFTWARELYS B:194 , HIS B:202 , HOH B:711 , TRP D:389 , ASN D:391 , HOH D:879binding site for residue EDO B 403
25AE7SOFTWARESER B:42 , SER B:43 , HIS B:44 , PRO B:45 , SER B:48 , LYS D:565binding site for residue EDO B 405
26AE8SOFTWAREASN B:94 , LEU B:188 , LYS B:189 , SER B:191 , LYS B:194 , HOH B:778binding site for residue EDO B 406
27AE9SOFTWARELYS B:199 , ASP B:204 , GLN B:206 , EDO B:412binding site for residue EDO B 407
28AF1SOFTWAREPHE B:353 , ILE B:356 , GLN B:357 , PRO B:358 , HOH B:616binding site for residue EDO B 408
29AF2SOFTWARELYS B:262 , ASP B:334 , GLU C:444 , HOH C:944binding site for residue EDO B 409
30AF3SOFTWARELYS B:109 , GLU B:241 , LYS B:245 , HOH B:682binding site for residue EDO B 410
31AF4SOFTWARELYS B:33 , ASN B:34 , GLN B:52 , HOH B:519binding site for residue EDO B 411
32AF5SOFTWARELEU B:203 , ASP B:204 , EDO B:407 , ARG D:388binding site for residue EDO B 412
33AF6SOFTWARELEU B:180 , ARG B:184 , PHE B:197 , PHE B:198 , ASP B:204 , TYR B:205binding site for residue EDO B 413
34AF7SOFTWAREALA A:27 , HOH A:597 , ALA B:27 , SER C:499 , SER D:499 , HOH D:806 , HOH D:854 , HOH D:864binding site for residue EDO D 702
35AF8SOFTWAREASP D:510 , GLU D:511 , GLN D:533binding site for residue EDO D 703
36AF9SOFTWARELEU A:304 , ALA D:521 , ASP D:525 , HOH D:880 , HOH D:917binding site for residue EDO D 704
37AG1SOFTWAREPRO D:501 , ARG D:502 , PHE D:503 , ILE D:514 , GLU D:515 , GLY D:518 , HOH D:814 , HOH D:856binding site for residue EDO D 705
38AG2SOFTWARETYR A:29 , PRO B:30 , ILE B:32 , SER D:495 , SER D:560 , THR D:561 , HOH D:801 , HOH D:815binding site for residue EDO D 706
39AG3SOFTWAREASN B:311 , SER D:485 , TYR D:490 , HOH D:807 , HOH D:846binding site for residue EDO D 707
40AG4SOFTWAREARG B:326 , ASP D:422 , PHE D:423 , ASN D:429 , ASN D:431 , LEU D:435 , ASN D:441 , HOH D:850 , HOH D:862 , HOH D:911binding site for residue EDO D 708
41AG5SOFTWAREASP D:387 , ARG D:388 , TRP D:389 , GLY D:390 , SER D:555 , PHE D:557 , HOH D:852 , HOH D:873 , HOH D:897binding site for residue EDO D 709
42AG6SOFTWAREASN C:526 , HOH C:841 , ASP D:522 , ASP D:525 , HOH D:818binding site for residue EDO D 710
43AG7SOFTWAREARG D:475 , ARG D:513binding site for residue EDO D 711
44AG8SOFTWAREALA B:79 , ARG B:103 , THR D:381 , TYR D:397 , THR D:398 , ASN D:400 , GLU D:419 , ASP D:422 , TYR D:433 , SER D:451 , SER D:452 , MET D:453 , PRO D:471 , GLY D:472 , GLY D:473 , ILE D:476 , HOH D:855 , HOH D:857 , HOH D:860 , HOH D:914binding site for Di-peptide 4UD D 701 and THR D 380
45AG9SOFTWAREALA B:79 , ARG B:103 , THR D:381 , TYR D:397 , THR D:398 , ASN D:400 , GLU D:419 , ASP D:422 , TYR D:433 , SER D:451 , SER D:452 , MET D:453 , PRO D:471 , GLY D:472 , GLY D:473 , ILE D:476 , HOH D:855 , HOH D:857 , HOH D:860 , HOH D:914binding site for Di-peptide 4UD D 701 and THR D 380

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5BPK)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Pro A:281 -Pro A:282
2Leu C:508 -Pro C:509
3Pro B:281 -Pro B:282
4Leu D:508 -Pro D:509

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5BPK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5BPK)

(-) Exons   (0, 0)

(no "Exon" information available for 5BPK)

(-) 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:348
                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eee...eeee..hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh........eeeeeee.....eeeeee...........................hhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhee.hhhhhhhhhhhhhhhh.hhhhhhhhee...ee.....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhh...eee..eeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh.......hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5bpk A  27 ASYPPIKNTKVGLALSSHPLASEIGQKVLEEGGNAIDAAVAIGFALAVVHPAAGNIGGGGFAVIHLANGENVALDFREKAPLKATKNMFLDKQGNVVPKLSEDGYLAAGVPGTVAGMEAMLKKYGTKKLSQLIDPAIKLAENGYAISQRQAETLKEARERFLKYSSSKKYFFKKGHLDYQEGDLFVQKDLAKTLNQIKTLGAKGFYQGQVAELIEKDMKKNGGIITKEDLASYNVKWRKPVVGSYRGYKIISMSPPSSGGTHLIQILNVMENADLSALGYGASKNIHIAAEAMRQAYADRSVYMGDADFVSVPVDKLINKAYAKKIFDTIQPDTVTPSSQIKPGMGQL 374
                                    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        


Chain B from PDB  Type:PROTEIN  Length:348
                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eee...eeee..hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh........eeeeeee.....eeeeee...................................hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhee.hhhhhhhhhhhhhhhh.hhhhhhhh............ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhh...eee..eeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh.......hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5bpk B  27 ASYPPIKNTKVGLALSSHPLASEIGQKVLEEGGNAIDAAVAIGFALAVVHPAAGNIGGGGFAVIHLANGENVALDFREKAPLKATKNMFLDKQGNVVPKLSEDGYLAAGVPGTVAGMEAMLKKYGTKKLSQLIDPAIKLAENGYAISQRQAETLKEARERFLKYSSSKKYFFKKGHLDYQEGDLFVQKDLAKTLNQIKTLGAKGFYQGQVAELIEKDMKKNGGIITKEDLASYNVKWRKPVVGSYRGYKIISMSPPSSGGTHLIQILNVMENADLSALGYGASKNIHIAAEAMRQAYADRSVYMGDADFVSVPVDKLINKAYAKKIFDTIQPDTVTPSSQIKPGMGQL 374
                                    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        


Chain C from PDB  Type:PROTEIN  Length:188
                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee....eeeeeee...................hhhhhh................................eeeee..eeeeee...hhhhhhhhhhhhhhhhhh...hhhhhhhh...........eee.....hhhhhhhhhhhh..eee........eeeeee....eeeeee.hhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bpk C 380 TTHYSVADRWGNAVSVTYTINASYGSAASIDGAGFLLNNEMDDFSIKPGNPNLYGLVGGDANAIEANKRPLSSMSPTIVLKNNKVFLVVGSPGGSRIITTVLQVISNVIDYNMNISEAVSAPRFHMQWLPDELRIEKFGMPADVKDNLTKMGYQIVTKPVMGDVNAIQVLPKTKGSVFYGSTDPRKEF 567
                                   389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559        


Chain D from PDB  Type:PROTEIN  Length:188
                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee....eeeeeee...................hhhhhh................................eeeee..eeeeee...hhhhhhhhhhhhhhhhhh...hhhhhhhh...........eee.....hhhhhhhhhhh...eee........eeeeee....eeeeee.hhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bpk D 380 TTHYSVADRWGNAVSVTYTINASYGSAASIDGAGFLLNNEMDDFSIKPGNPNLYGLVGGDANAIEANKRPLSSMSPTIVLKNNKVFLVVGSPGGSRIITTVLQVISNVIDYNMNISEAVSAPRFHMQWLPDELRIEKFGMPADVKDNLTKMGYQIVTKPVMGDVNAIQVLPKTKGSVFYGSTDPRKEF 567
                                   389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559
   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  (0, 0)

(no "SCOP Domain" information available for 5BPK)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5BPK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5BPK)

(-) Gene Ontology  (5, 5)

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UniProtKB/TrEMBL
        O25743_HELPY | O25743: 2nqo 2qm6 2qmc 3fnm

(-) Related Entries Specified in the PDB File

3fnm HELICOBACTER PYLORI GGT