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(-) Description

Title :  MEMBRANE PROTEIN AT 2.8 ANGSTROMS
 
Authors :  L. Vogeley, T. El Arnaout, J. Bailey, C. Boland, M. Caffrey
Date :  01 Sep 15  (Deposition) - 02 Mar 16  (Release) - 09 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Membrane Protein, Protease, Antibiotic, Complex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Vogeley, T. El Arnaout, J. Bailey, P. J. Stansfeld, C. Boland, M. Caffrey
Structural Basis Of Lipoprotein Signal Peptidase Ii Action And Inhibition By The Antibiotic Globomycin.
Science V. 351 876 2016
PubMed-ID: 26912896  |  Reference-DOI: 10.1126/SCIENCE.AAD3747

(-) Compounds

Molecule 1 - LIPOPROTEIN SIGNAL PEPTIDASE
    Chains: A, B, C, D
    EC Number: 3.4.23.36
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28A
    Expression System Taxid: 469008
    Expression System Variant: C41
    Gene: LSPA, LS, PA4559
    Organism Scientific: PSEUDOMONAS AERUGINOSA (STRAIN ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)
    Organism Taxid: 208964
    Other Details: N-TERMINAL 6XHIS TAG AND THROMBIN SITE
    Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228
    Synonym: PROLIPOPROTEIN SIGNAL PEPTIDASE,SIGNAL PEPTIDASE II,SPASE II

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 44)

Asymmetric Unit (6, 44)
No.NameCountTypeFull Name
15BV4Ligand/Ion(2R,3R)-3-(GLYCYLOXY)-2-METHYLNONANOIC ACID
2ALO4Ligand/IonALLO-THREONINE
3IIL4Ligand/IonISO-ISOLEUCINE
4MLE4Ligand/IonN-METHYLLEUCINE
5OLC24Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE
6SER4Mod. Amino AcidSERINE
Biological Unit 1 (6, 11)
No.NameCountTypeFull Name
15BV1Ligand/Ion(2R,3R)-3-(GLYCYLOXY)-2-METHYLNONANOIC ACID
2ALO1Ligand/IonALLO-THREONINE
3IIL1Ligand/IonISO-ISOLEUCINE
4MLE1Ligand/IonN-METHYLLEUCINE
5OLC6Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE
6SER1Mod. Amino AcidSERINE
Biological Unit 2 (6, 12)
No.NameCountTypeFull Name
15BV1Ligand/Ion(2R,3R)-3-(GLYCYLOXY)-2-METHYLNONANOIC ACID
2ALO1Ligand/IonALLO-THREONINE
3IIL1Ligand/IonISO-ISOLEUCINE
4MLE1Ligand/IonN-METHYLLEUCINE
5OLC7Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE
6SER1Mod. Amino AcidSERINE
Biological Unit 3 (6, 11)
No.NameCountTypeFull Name
15BV1Ligand/Ion(2R,3R)-3-(GLYCYLOXY)-2-METHYLNONANOIC ACID
2ALO1Ligand/IonALLO-THREONINE
3IIL1Ligand/IonISO-ISOLEUCINE
4MLE1Ligand/IonN-METHYLLEUCINE
5OLC6Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE
6SER1Mod. Amino AcidSERINE
Biological Unit 4 (6, 10)
No.NameCountTypeFull Name
15BV1Ligand/Ion(2R,3R)-3-(GLYCYLOXY)-2-METHYLNONANOIC ACID
2ALO1Ligand/IonALLO-THREONINE
3IIL1Ligand/IonISO-ISOLEUCINE
4MLE1Ligand/IonN-METHYLLEUCINE
5OLC5Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE
6SER1Mod. Amino AcidSERINE

(-) Sites  (28, 28)

Asymmetric Unit (28, 28)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREILE A:100 , PHE A:139 , ASP A:143 , THR A:147 , VAL A:148 , SER A:203 , ALO A:204 , OLC A:209binding site for residue OLC A 206
02AC2SOFTWARESER A:26 , PHE A:29 , GLU A:33 , ILE A:40 , TRP A:49 , LEU A:141 , OLC A:208binding site for residue OLC A 207
03AC3SOFTWAREVAL A:41 , TRP A:49 , OLC A:207binding site for residue OLC A 208
04AC4SOFTWAREVAL A:4 , GLY A:8 , PRO A:11 , TRP A:12 , ILE A:15 , LYS A:93 , OLC A:206 , VAL D:25 , ALA D:32binding site for residue OLC A 209
05AC5SOFTWARELEU A:10 , PRO A:11 , TRP A:14 , PHE A:20 , GLN D:31 , TYR D:114binding site for residue OLC A 210
06AC6SOFTWAREPHE A:20 , ARG A:70 , MET A:117 , VAL B:42 , OLC B:211binding site for residue OLC A 211
07AC7SOFTWARETHR B:55 , PHE B:136 , PRO B:137 , ALA B:138 , PHE B:139 , VAL B:148 , IIL B:202 , ALO B:204 , OLC B:207 , OLC B:208binding site for residue OLC B 206
08AC8SOFTWAREPHE B:136 , THR B:147 , VAL B:151 , ALA B:154 , OLC B:206binding site for residue OLC B 207
09AC9SOFTWAREILE B:40 , VAL B:42 , TRP B:49 , OLC B:206 , OLC B:212binding site for residue OLC B 208
10AD1SOFTWAREGLY B:8 , ARG B:9 , PRO B:11 , TRP B:12 , LYS B:93 , LEU B:104 , ALA C:32binding site for residue OLC B 209
11AD2SOFTWAREPHE B:7 , TRP B:14 , VAL B:17 , TRP C:14 , ALA C:28 , TYR C:114binding site for residue OLC B 210
12AD3SOFTWAREALA A:63 , ASP A:64 , SER A:65 , TRP A:71 , OLC A:211 , TRP B:130 , TRP B:134binding site for residue OLC B 211
13AD4SOFTWARELEU B:22 , SER B:26 , GLU B:33 , ILE B:40 , TRP B:49 , OLC B:208binding site for residue OLC B 212
14AD5SOFTWAREVAL C:19 , PRO C:137 , PHE C:139 , ASP C:143 , THR C:147 , VAL C:148 , SER C:203 , ALO C:204 , OLC C:211binding site for residue OLC C 206
15AD6SOFTWARELEU C:153 , ALO C:204 , 5BV C:205binding site for residue OLC C 207
16AD7SOFTWAREVAL C:41 , VAL C:42 , OLC C:211binding site for residue OLC C 208
17AD8SOFTWAREPHE C:20 , LEU C:110 , TYR C:114 , MET C:117 , VAL C:118 , OLC C:210binding site for residue OLC C 209
18AD9SOFTWAREARG C:70 , ILE C:78 , VAL C:85 , MET C:117 , OLC C:209 , OLC D:209 , OLC D:210binding site for residue OLC C 210
19AE1SOFTWAREPHE C:29 , ILE C:40 , TRP C:49 , OLC C:206 , OLC C:208binding site for residue OLC C 211
20AE2SOFTWAREPHE D:136 , PHE D:139 , ASP D:143 , THR D:147 , VAL D:148 , SER D:203 , ALO D:204binding site for residue OLC D 206
21AE3SOFTWARELEU D:22 , GLU D:33 , ILE D:40 , TRP D:49 , LEU D:141 , OLC D:208binding site for residue OLC D 207
22AE4SOFTWAREOLC D:207 , OLC D:209binding site for residue OLC D 208
23AE5SOFTWARESER C:65 , TRP C:71 , MET C:117 , OLC C:210 , TRP D:130 , OLC D:208 , OLC D:210binding site for residue OLC D 209
24AE6SOFTWAREOLC C:210 , ILE D:43 , TRP D:134 , OLC D:209binding site for residue OLC D 210
25AE7SOFTWAREASN A:54 , PHE A:59 , LEU A:62 , LEU A:72 , PHE A:73 , ASN A:112 , ARG A:116 , VAL A:122 , ASP A:124 , ASN A:140 , ASP A:143 , OLC A:206binding site for Ligand residues ALO A 204 through SER A 203 bound to SER A 203
26AE8SOFTWARETHR B:55 , PHE B:73 , ILE B:76 , ALA B:77 , ASN B:112 , ARG B:116 , VAL B:122 , ASP B:124 , ASP B:143 , ILE B:146 , THR B:147 , OLC B:206binding site for Ligand residues ALO B 204 through SER B 203 bound to SER B 203
27AE9SOFTWAREASN C:54 , GLY C:56 , PHE C:59 , PHE C:73 , ASN C:112 , ARG C:116 , VAL C:122 , ASP C:124 , ASN C:140 , ASP C:143 , OLC C:206 , OLC C:207binding site for Ligand residues ALO C 204 through SER C 203 bound to SER C 203
28AF1SOFTWAREASN D:54 , ALA D:57 , PHE D:59 , PHE D:73 , ILE D:76 , ALA D:77 , VAL D:80 , ASN D:112 , ARG D:116 , VAL D:122 , ASP D:124 , ASP D:143 , ILE D:146 , OLC D:206binding site for Ligand residues ALO D 204 through SER D 203 bound to SER D 203

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5DIR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DIR)

(-) 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:157
                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee...eeeeeeee....hhhhh....hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee...ee....hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dir A   2 PDVDRFGRLPWLWITVLVFVLDQVSKAFFQAELSMYQQIVVIPDLFSWTLAYNTGAAFSFLADSSGWQRWLFALIAIVVSASLVVWLKRLKKGETWLAIALALVLGGALGNLYDRMVLGHVVDFILVHWQNRWYFPAFNLADSAITVGAVMLALDMF 158
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       


Chain B from PDB  Type:PROTEIN  Length:149
                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee...eeeeeee.hhh....hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee...ee....hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dir B   2 PDVDRFGRLPWLWITVLVFVLDQVSKAFFQAELSMYQQIVVIPDLFSWTLAYNTGAAFSGWQRWLFALIAIVVSASLVVWLKRLKKGETWLAIALALVLGGALGNLYDRMVLGHVVDFILVHWQNRWYFPAFNLADSAITVGAVMLALD 156
                                    11        21        31        41        51        67        77        87        97       107       117       127       137       147         
                                                                                     60|                                                                                         
                                                                                      67                                                                                         


Chain C from PDB  Type:PROTEIN  Length:149
                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhh....eeeee...eeeeeeee....hhhhh....hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee...ee....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dir C  11 PWLWITVLVFVLDQVSKAFFQAELSMYQQIVVIPDLFSWTLAYNTGAAFSFLADSSGWQRWLFALIAIVVSASLVVWLKRLKKGETWLAIALALVLGGALGNLYDRMVLGHVVDFILVHWQNRWYFPAFNLADSAITVGAVMLALDMFR 159
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150         


Chain D from PDB  Type:PROTEIN  Length:149
                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh....eeeee...eeeeeeee.......hhhhh.hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee...ee....hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dir D  11 PWLWITVLVFVLDQVSKAFFQAELSMYQQIVVIPDLFSWTLAYNTGAAFSFLADSSGWQRWLFALIAIVVSASLVVWLKRLKKGETWLAIALALVLGGALGNLYDRMVLGHVVDFILVHWQNRWYFPAFNLADSAITVGAVMLALDMFR 159
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150
   Legend:   → Mismatch (orange background)
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  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 5DIR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

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