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(-) Description

Title :  CRYSTAL STRUCTURE OF AN ACTIVITY-BASED PROBE HNE COMPLEX
 
Authors :  B. C. Lechtenberg, P. Kasperkiewicz, H. R. Robinson, M. Drag, S. J. Ried
Date :  06 Nov 14  (Deposition) - 11 Feb 15  (Release) - 09 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.63
Chains :  Asym. Unit :  E,I
Biol. Unit 1:  E,I  (1x)
Biol. Unit 2:  E,I  (3x)
Keywords :  Neutrophil Elastase, Acitivity-Based Probe, Inhibitor, Protease, Complex, Hne, Hycosul, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. C. Lechtenberg, P. Kasperkiewicz, H. Robinson, M. Drag, S. J. Riedl
The Elastase-Pk101 Structure: Mechanism Of An Ultrasensitiv Activity-Based Probe Revealed.
Acs Chem. Biol. V. 10 945 2015
PubMed-ID: 25581168  |  Reference-DOI: 10.1021/CB500909N

(-) Compounds

Molecule 1 - NEUTROPHIL ELASTASE
    Chains: E
    EC Number: 3.4.21.37
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: BONE MARROW SERINE PROTEASE,ELASTASE-2,HUMAN LEUKOCYTE ELASTASE,HLE,MEDULLASIN,PMN ELASTASE
 
Molecule 2 - BTN-3V3-NLB-OMT-OIC-3V2
    Chains: I
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : EI
Biological Unit 1 (1x): EI
Biological Unit 2 (3x): EI

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (11, 22)

Asymmetric Unit (11, 22)
No.NameCountTypeFull Name
13V21OTHER[(1R)-1-AMINOPROPYL]PHOSPHONIC ACID
23V31OTHER1-AMINO-3,6,9,12-TETRAOXAPENTADECAN-15-OIC ACID
3BMA1Ligand/IonBETA-D-MANNOSE
4BTN1OTHERBIOTIN
5EDO6Ligand/Ion1,2-ETHANEDIOL
6FUC2Ligand/IonALPHA-L-FUCOSE
7NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
8NLB1OTHER6-(BENZYLOXY)-L-NORLEUCINE
9OIC1OTHEROCTAHYDROINDOLE-2-CARBOXYLIC ACID
10OMT1Mod. Amino AcidS-DIOXYMETHIONINE
11SO43Ligand/IonSULFATE ION
Biological Unit 1 (11, 22)
No.NameCountTypeFull Name
13V21OTHER[(1R)-1-AMINOPROPYL]PHOSPHONIC ACID
23V31OTHER1-AMINO-3,6,9,12-TETRAOXAPENTADECAN-15-OIC ACID
3BMA1Ligand/IonBETA-D-MANNOSE
4BTN1OTHERBIOTIN
5EDO6Ligand/Ion1,2-ETHANEDIOL
6FUC2Ligand/IonALPHA-L-FUCOSE
7NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
8NLB1OTHER6-(BENZYLOXY)-L-NORLEUCINE
9OIC1OTHEROCTAHYDROINDOLE-2-CARBOXYLIC ACID
10OMT1Mod. Amino AcidS-DIOXYMETHIONINE
11SO43Ligand/IonSULFATE ION
Biological Unit 2 (11, 66)
No.NameCountTypeFull Name
13V23OTHER[(1R)-1-AMINOPROPYL]PHOSPHONIC ACID
23V33OTHER1-AMINO-3,6,9,12-TETRAOXAPENTADECAN-15-OIC ACID
3BMA3Ligand/IonBETA-D-MANNOSE
4BTN3OTHERBIOTIN
5EDO18Ligand/Ion1,2-ETHANEDIOL
6FUC6Ligand/IonALPHA-L-FUCOSE
7NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE
8NLB3OTHER6-(BENZYLOXY)-L-NORLEUCINE
9OIC3OTHEROCTAHYDROINDOLE-2-CARBOXYLIC ACID
10OMT3Mod. Amino AcidS-DIOXYMETHIONINE
11SO49Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG E:21 , LEU E:144 , ARG E:148 , ALA E:152 , SER E:153 , VAL E:154 , GLN E:156 , HOH E:671binding site for residue SO4 E 408
02AC2SOFTWAREARG E:36 , ASN E:132 , VAL E:163 , THR E:164 , SER E:165 , HOH E:557 , HOH E:572binding site for residue SO4 E 409
03AC3SOFTWAREGLU E:90 , ASN E:92 , GLY E:93 , TYR E:94 , HOH E:525 , HOH E:689binding site for residue EDO E 410
04AC4SOFTWAREARG E:177 , ARG E:178 , SER E:179 , HOH E:538binding site for residue EDO E 411
05AC5SOFTWAREARG E:75 , ARG E:76binding site for residue EDO E 412
06AC6SOFTWAREASN E:115 , ALA E:116 , NAG E:401 , FUC E:402 , NAG E:403 , HOH E:520binding site for residue EDO E 413
07AC7SOFTWAREARG E:21 , ALA E:22 , HIS E:71 , VAL E:154 , HOH E:503 , HOH E:523binding site for residue EDO E 414
08AC8SOFTWAREGLN E:126 , ASN E:236 , HOH E:505 , HOH E:565binding site for residue EDO E 415
09AC9SOFTWARE3V3 I:102 , OMT I:104 , HOH I:301binding site for residue SO4 I 201
10AD1SOFTWAREARG E:63B , VAL E:64 , ARG E:65 , ALA E:84 , ASN E:109binding site for Poly-Saccharide residues NAG E 405 through NAG E 407 bound to ASN E 109
11AD2SOFTWARETRP E:27 , GLN E:135 , ASN E:159 , VAL E:200 , CYS E:201 , ASN E:202 , GLY E:207 , HOH E:517 , HOH E:526 , HOH E:539 , HOH E:552 , HOH E:554 , HOH E:612 , BTN I:101binding site for Poly-Saccharide residues NAG E 401 through BMA E 404 bound to ASN E 159
12AD3SOFTWAREHIS E:57 , CYS E:58 , ALA E:60 , ASN E:61 , VAL E:62 , VAL E:97 , ASN E:98 , LEU E:166 , CYS E:168 , ARG E:177 , CYS E:191 , PHE E:192 , GLY E:193 , ASP E:194 , SER E:195 , SER E:214 , PHE E:215 , VAL E:216 , ARG E:217 , GLY E:218 , GLY E:219 , TYR E:224 , BMA E:404 , SO4 I:201 , HOH I:301 , HOH I:302 , HOH I:303 , HOH I:304 , HOH I:305 , HOH I:306 , HOH I:309 , HOH I:310binding site for ? chain I

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1E:42 -E:58
2E:136 -E:201
3E:168 -E:182
4E:191 -E:220

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4WVP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4WVP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4WVP)

(-) Exons   (0, 0)

(no "Exon" information available for 4WVP)

(-) 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 E from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                           
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeee..eeeeeeeeee..eeeehhhhh...hhh.eeeee............eeeeeeeeee............eeeee..........................eeeeee..............eeeeeeee........eeee...............eeee..eeeeeeeee..........eeeee...hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4wvp E   16 IVGGRRARPHAWPFMVSLQLRGGHFCGATLIAPNFVMSAAHCVANVNVRAVRVVLGAHNLSRREPTRQVFAVQRIFENGYDPVNLLNDIVILQLNGSATINANVQVAQLPAQGRRLGNGVQCLAMGWGLLGRNRGIASVLQELNVTVVTSLCRRSNVCTLVRGRQAGVCFGDSGSPLVCNGLIHGIASFVRGGCASGLYPDAFAPVAQFVNWIDSIIQ  243
                                    25        35||      46        56       63C        73        83      ||94       104       114       124       134       144   ||  155       165|||    184  ||   192       202|      216    |  225       235        
                                               36|                       63A||                         90|                                                     148|             166||      186A|             202|          220A                       
                                                38                        63B|                          92                                                      150              168|       186B              207                                     
                                                                           63C                                                                                                    177                                                                 


Chain I from PDB  Type:OTHER/PROTEIN  Length:6
                                       
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...ee. Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                4wvp I  101 xxxmxx  106
                            ||||||
                          101-BTN|
                           102-3V3
                            103-NLB
                             104-OMT
                              105-OIC
                               106-3V2
   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 4WVP)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4WVP)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4WVP)

(-) Gene Ontology  (40, 40)

Asymmetric Unit(hide GO term definitions)

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        ELNE_HUMAN | P08246: 1b0f 1h1b 1hne 1ppf 1ppg 2rg3 2z7f 3q76 3q77 4nzl 5a09 5a0a 5a0b 5a0c 5a8x 5a8y 5a8z 5abw

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