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(-) Description

Title :  THE X-RAY CRYSTAL STRUCTURE OF A DIMERIC VARIANT OF HUMAN PANCREATIC RIBONUCLEASE
 
Authors :  A. Pica, A. Merlino, L. Mazzarella, F. Sica
Date :  26 May 13  (Deposition) - 02 Oct 13  (Release) - 24 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Pica, A. Merlino, A. K. Buell, T. P. Knowles, E. Pizzo, G. D'Alessio, F. Sica, L. Mazzarella
Three-Dimensional Domain Swapping And Supramolecular Protei Assembly: Insights From The X-Ray Structure Of A Dimeric Swapped Variant Of Human Pancreatic Rnase.
Acta Crystallogr. , Sect. D V. 69 2116 2013
PubMed-ID: 24100329  |  Reference-DOI: 10.1107/S0907444913020507

(-) Compounds

Molecule 1 - RIBONUCLEASE PANCREATIC
    Chains: A, B, C, D
    EC Number: 3.1.27.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 29-151
    Gene: RNASE1, RIB1, RNS1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HP-RNASE, RIB-1, RNASE UPI-1, RIBONUCLEASE 1, RNASE 1, RIBONUCLEASE A, RNASE A

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 17)

Asymmetric Unit (3, 17)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2NA3Ligand/IonSODIUM ION
3SO413Ligand/IonSULFATE ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NA-1Ligand/IonSODIUM ION
3SO46Ligand/IonSULFATE ION
Biological Unit 2 (1, 7)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NA-1Ligand/IonSODIUM ION
3SO47Ligand/IonSULFATE ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:119 , PHE A:120 , HOH A:354 , GLN B:11 , HIS B:12BINDING SITE FOR RESIDUE SO4 A 201
02AC2SOFTWAREARG A:32 , ARG A:33BINDING SITE FOR RESIDUE SO4 A 202
03AC3SOFTWAREGLN A:11 , HIS A:12 , HIS B:119 , PHE B:120 , HOH B:316 , HOH B:329BINDING SITE FOR RESIDUE SO4 B 201
04AC4SOFTWAREHIS A:12 , LYS B:41 , VAL B:43 , ASN B:44 , THR B:45 , PHE B:120 , HOH B:329BINDING SITE FOR RESIDUE SO4 B 202
05AC5SOFTWAREARG B:32 , ARG B:33 , HOH B:310 , HOH B:346BINDING SITE FOR RESIDUE SO4 B 203
06AC6SOFTWAREARG B:32 , SER D:113BINDING SITE FOR RESIDUE SO4 B 204
07AC7SOFTWAREHOH A:306 , HOH A:315 , LEU B:51 , HOH B:324 , LEU C:51BINDING SITE FOR RESIDUE NA B 205
08AC8SOFTWARELYS C:41 , HIS C:119 , PHE C:120 , HOH C:324 , GLN D:11 , HIS D:12BINDING SITE FOR RESIDUE SO4 C 201
09AC9SOFTWAREGLN C:11 , HIS C:12 , LYS D:41 , HIS D:119 , PHE D:120BINDING SITE FOR RESIDUE SO4 C 202
10BC1SOFTWAREARG C:32 , ARG C:33BINDING SITE FOR RESIDUE SO4 C 203
11BC2SOFTWAREARG B:91 , ARG C:10 , GLN C:11 , ASN D:34 , ARG D:39 , HOH D:305BINDING SITE FOR RESIDUE SO4 C 204
12BC3SOFTWAREARG A:91 , ASN C:34 , ARG C:39 , HOH C:322BINDING SITE FOR RESIDUE SO4 C 205
13BC4SOFTWAREHOH A:313 , HOH A:320 , HOH A:325 , GLN C:28BINDING SITE FOR RESIDUE NA C 206
14BC5SOFTWARETYR C:92BINDING SITE FOR RESIDUE CL C 207
15BC6SOFTWARELYS B:6 , ARG D:32 , ARG D:33 , HOH D:325BINDING SITE FOR RESIDUE SO4 D 201
16BC7SOFTWAREARG D:85 , THR D:87 , ASN D:88 , ARG D:98 , HOH D:324BINDING SITE FOR RESIDUE SO4 D 202
17BC8SOFTWAREPRO A:50 , LEU A:51 , HOH A:301 , HOH C:337 , HOH D:340BINDING SITE FOR RESIDUE NA D 203

(-) SS Bonds  (16, 16)

Asymmetric Unit
No.Residues
1A:72 -A:65
2A:84 -A:26
3A:95 -A:40
4A:110 -A:58
5B:72 -B:65
6B:84 -B:26
7B:95 -B:40
8B:110 -B:58
9C:72 -C:65
10C:84 -C:26
11C:95 -C:40
12C:110 -C:58
13D:72 -D:65
14D:84 -D:26
15D:95 -D:40
16D:110 -D:58

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Tyr A:92 -Pro A:93
2Ser A:113 -Pro A:114
3Tyr B:92 -Pro B:93
4Ser B:113 -Pro B:114
5Tyr C:92 -Pro C:93
6Ser C:113 -Pro C:114
7Tyr D:92 -Pro D:93
8Ser D:113 -Pro D:114

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KXH)

(-) 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:120
                                                                                                                                                        
               SCOP domains d4kxha_ A: Ribonuclease A (also ribonuclease B, S)                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeee..hhhhhhhhhhheee........eee....eeeeeeee..........eeeeeeeeeeeeeee....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 4kxh A   1 KESRAKKFQRQHMDSSSSTYCNQMMRRRNMTQGRCKPVNTFVHEPLVDVQNVCFQEKVTCKNGQGNCYKSNSSMHITDCRLTNGSRYPNCAYRTSPKERHIIVACEGSPYVPVHFDASVE 125
                                    10    ||  25        35        45        55        65        75        85        95       105       115       125
                                         15|                                                                                                        
                                          21                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:120
                                                                                                                                                        
               SCOP domains d4kxhb_ B: Ribonuclease A (also ribonuclease B, S)                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeee..hhhhhhhhhhheee........eee....eeeeeeee..........eeeeeeeeeeeeeee....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 4kxh B   1 KESRAKKFQRQHMDSSSSTYCNQMMRRRNMTQGRCKPVNTFVHEPLVDVQNVCFQEKVTCKNGQGNCYKSNSSMHITDCRLTNGSRYPNCAYRTSPKERHIIVACEGSPYVPVHFDASVE 125
                                    10    ||  25        35        45        55        65        75        85        95       105       115       125
                                         15|                                                                                                        
                                          21                                                                                                        


Chain C from PDB  Type:PROTEIN  Length:120
                                                                                                                                                        
               SCOP domains d4kxhc_ C: Ribonuclease A (also ribonuclease B, S)                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeee..hhhhhhhhhhheee........eee....eeeeeeee..........eeeeeeeeeeeeeee....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 4kxh C   1 KESRAKKFQRQHMDSSSSTYCNQMMRRRNMTQGRCKPVNTFVHEPLVDVQNVCFQEKVTCKNGQGNCYKSNSSMHITDCRLTNGSRYPNCAYRTSPKERHIIVACEGSPYVPVHFDASVE 125
                                    10    ||  25        35        45        55        65        75        85        95       105       115       125
                                         15|                                                                                                        
                                          21                                                                                                        


Chain D from PDB  Type:PROTEIN  Length:120
                                                                                                                                                        
               SCOP domains d4kxhd_ D: Ribonuclease A (also ribonuclease B, S)                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeee..hhhhhhhhhhheee........eee....eeeeeeee..........eeeeeeeeeeeeeee....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 4kxh D   1 KESRAKKFQRQHMDSSSSTYCNQMMRRRNMTQGRCKPVNTFVHEPLVDVQNVCFQEKVTCKNGQGNCYKSNSSMHITDCRLTNGSRYPNCAYRTSPKERHIIVACEGSPYVPVHFDASVE 125
                                    10    ||  25        35        45        55        65        75        85        95       105       115       125
                                         15|                                                                                                        
                                          21
   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  (1, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)

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        RNAS1_HUMAN | P07998: 1dza 1e21 1h8x 1z7x 2e0j 2e0l 2e0m 2e0o 2k11 2q4g 3f8g

(-) Related Entries Specified in the PDB File

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