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(-) Description

Title :  CRYSTAL STRUCTURE OF KALLIKREIN-RELATED PEPTIDASE 4
 
Authors :  O. V. Ilyichova, J. E. Swedberg, S. J. De Veer, K. C. Sit, J. M. Harris, A.
Date :  29 Apr 13  (Deposition) - 30 Apr 14  (Release) - 02 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.32
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Klk4, Kallikrein-4, Serine Protease, Protease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. T. Riley, O. Ilyichova, M. G. S. Costa, B. T. Porebski, S. J. De Veer, J. E. Swedberg, I. Kass, J. M. Harris, D. E. Hoke, A. M. Buckle
Direct And Indirect Mechanisms Of Klk4 Inhibition Revealed By Structure And Dynamics
Sci Rep V. 6 35385 2016
PubMed-ID: 27767076  |  Reference-DOI: 10.1038/SREP35385

(-) Compounds

Molecule 1 - KALLIKREIN-4
    Chains: A, B
    EC Number: 3.4.21.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET12A-PROPSA-HK4
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RELATED PEPTIDASE 4, UNP RESIDUES 31-253
    Gene: KLK4
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ENAMEL MATRIX SERINE PROTEINASE 1, KALLIKREIN-LIKE PROTEIN 1, KLK-L1, PROSTASE, SERINE PROTEASE 17

 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  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2NI4Ligand/IonNICKEL (II) ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2NI-1Ligand/IonNICKEL (II) ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2NI-1Ligand/IonNICKEL (II) ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:25 , GLU A:77 , HOH A:405 , HOH A:416BINDING SITE FOR RESIDUE NI A 301
2AC2SOFTWAREHIS A:57 , GLN A:186A , SER A:195 , SER A:214 , HOH A:415 , HOH A:427BINDING SITE FOR RESIDUE NI A 302
3AC3SOFTWAREHIS B:57 , GLN B:186A , SER B:195BINDING SITE FOR RESIDUE NI B 301
4AC4SOFTWAREHIS B:25 , GLU B:77 , HOH B:416 , HOH B:417BINDING SITE FOR RESIDUE NI B 302
5AC5SOFTWARELYS B:217 , VAL B:222BINDING SITE FOR RESIDUE EDO B 303

(-) SS Bonds  (12, 12)

Asymmetric Unit
No.Residues
1A:22 -A:157
2A:42 -A:58
3A:128 -A:232
4A:136 -A:201
5A:168 -A:182
6A:191 -A:220
7B:22 -B:157
8B:42 -B:58
9B:128 -B:232
10B:136 -B:201
11B:168 -B:182
12B:191 -B:220

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Arg A:96 -Pro A:97
2Asp A:173 -Pro A:174
3Ala A:218 -Pro A:219
4Arg B:96 -Pro B:97
5Asp B:173 -Pro B:174
6Ala B:218 -Pro B:219

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KGA)

(-) 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:221
                                                                                                                                                                                                                                                              
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeee..eeeeeeeeee..eeeehhhhh...eeeee...........eeeee.eeee.............eeee.........................eeeeee.............eeeeee..hhhhhhhhh.......eeee................eeee..eeeeeeee...........eeeee...hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4kga A   16 IINGEDCSPHSQPWQAALVMENELFCSGVLVHPQWVLSAAHCFQNSYTIGLGLHSLEQEPGSQMVEASLSVRHPEYNRPLLANDLMLIKLDESVSESDTIRSISIASQCPTAGNSCLVSGWGLLANGRMPTVLQCVNVSVVSEEVCSKLYDPLYHPSMFCAGGGQDQKDSCNGDSGGPLICNGYLQGLVSFGKAPCGQVGVPGVYTNLCKFTEWIEKTVQA  244
                                    25        35  ||    46        56        66||    ||78        88        98       108       118      |129||     140      |152       162       172       182    || 190       200  ||   214      |223       233       243 
                                                 38|                         67|   74|                                              125|  ||            147|                                 186A|              203|         220A                        
                                                  40                          69    76                                               127  ||             150                                  186B               208                                     
                                                                                                                                        130|                                                                                                             
                                                                                                                                         132                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                              
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeee..eeeeeeeeee..eeeehhhhh...eeee.............eeee.eeee.............eeee.........................eeeeee.............eeeeee..hhhhhhhhh.......eeee................eeee..eeeeeeee...........eeeee...hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4kga B   16 IINGEDCSPHSQPWQAALVMENELFCSGVLVHPQWVLSAAHCFQNSYTIGLGLHSLDQEPGSQMVEASLSVRHPEYNRPLLANDLMLIKLDESVSESDTIRSISIASQCPTAGNSCLVSGWGLLANGRMPTVLQCVNVSVVSEEVCSKLYDPLYHPSMFCAGGGQDQKDSCNGDSGGPLICNGYLQGLVSFGKAPCGQVGVPGVYTNLCKFTEWIEKTVQA  244
                                    25        35  ||    46        56        66||   || 78        88        98       108       118      |129||     140      |152       162       172       182    || 190       200  ||   214      |223       233       243 
                                                 38|                         67|  73|                                               125|  ||            147|                                 186A|              203|         220A                        
                                                  40                          69   75                                                127  ||             150                                  186B               208                                     
                                                                                                                                        130|                                                                                                             
                                                                                                                                         132
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4KGA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)

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  3.4.21.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        KLK4_HUMAN | Q9Y5K2: 2bdg 2bdh 2bdi 4k1e 4k8y 4kel

(-) Related Entries Specified in the PDB File

2bdg 2bdh 2bdi 4k1e 4k8y 4kel