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(-) Description

Title :  HUMAN ANGIOGENIN PD VARIANT Q77P
 
Authors :  W. J. Bradshaw, S. Rehman, T. T. K. Pham, N. Thiyagarajan, R. L. Lee, V. Subramanian, K. R. Acharya
Date :  01 Nov 16  (Deposition) - 22 Feb 17  (Release) - 22 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
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 :  Parkinson'S, Rnase, Angiogenesis, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. J. Bradshaw, S. Rehman, T. T. Pham, N. Thiyagarajan, R. L. Lee, V. Subramanian, K. R. Acharya
Structural Insights Into Human Angiogenin Variants Implicated In Parkinson'S Disease And Amyotrophic Lateral Sclerosis.
Sci Rep V. 7 41996 2017
PubMed-ID: 28176817  |  Reference-DOI: 10.1038/SREP41996

(-) Compounds

Molecule 1 - ANGIOGENIN
    Chains: A, B, C, D
    EC Number: 3.1.27.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Gene: ANG, RNASE5
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: RIBONUCLEASE 5,RNASE 5

 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  (4, 19)

Asymmetric Unit (4, 19)
No.NameCountTypeFull Name
1BTB1Ligand/Ion2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2EDO4Ligand/Ion1,2-ETHANEDIOL
3PGE2Ligand/IonTRIETHYLENE GLYCOL
4SO412Ligand/IonSULFATE ION
Biological Unit 1 (4, 6)
No.NameCountTypeFull Name
1BTB1Ligand/Ion2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2EDO2Ligand/Ion1,2-ETHANEDIOL
3PGE1Ligand/IonTRIETHYLENE GLYCOL
4SO42Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1BTB-1Ligand/Ion2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2EDO-1Ligand/Ion1,2-ETHANEDIOL
3PGE-1Ligand/IonTRIETHYLENE GLYCOL
4SO42Ligand/IonSULFATE ION
Biological Unit 3 (2, 6)
No.NameCountTypeFull Name
1BTB-1Ligand/Ion2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2EDO2Ligand/Ion1,2-ETHANEDIOL
3PGE-1Ligand/IonTRIETHYLENE GLYCOL
4SO44Ligand/IonSULFATE ION
Biological Unit 4 (2, 5)
No.NameCountTypeFull Name
1BTB-1Ligand/Ion2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2EDO-1Ligand/Ion1,2-ETHANEDIOL
3PGE1Ligand/IonTRIETHYLENE GLYCOL
4SO44Ligand/IonSULFATE ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:84 , ARG A:95 , HOH A:302binding site for residue SO4 A 201
02AC2SOFTWAREARG A:32 , ARG A:33 , HOH A:328binding site for residue SO4 A 202
03AC3SOFTWAREPRO A:38 , CYS A:39 , LYS A:40 , ASP A:41 , SER C:4binding site for residue PGE A 203
04AC4SOFTWAREARG A:101 , ILE A:119binding site for residue EDO A 204
05AC5SOFTWAREHIS A:13 , VAL A:113 , HIS A:114 , LEU A:115 , HOH A:320 , HOH A:335 , HOH A:354binding site for residue EDO A 205
06AC6SOFTWAREASN A:49 , LYS A:50 , ARG A:51 , HOH A:363 , ARG D:66binding site for residue BTB A 206
07AC7SOFTWAREARG B:32 , ARG B:33binding site for residue SO4 B 201
08AC8SOFTWARESER B:28 , ARG B:31 , ARG B:32 , HOH B:333binding site for residue SO4 B 202
09AC9SOFTWAREARG C:32 , ARG C:33 , HOH C:311 , HOH C:346binding site for residue SO4 C 201
10AD1SOFTWAREARG B:5 , HIS B:8 , LYS C:17 , HOH C:321 , TRP D:89binding site for residue SO4 C 202
11AD2SOFTWAREASN C:49 , LYS C:50 , ARG C:51binding site for residue SO4 C 203
12AD3SOFTWARETRP A:89 , LYS B:17 , HIS C:8 , HOH C:314 , HOH C:322binding site for residue SO4 C 204
13AD4SOFTWARESER C:28 , ARG C:31 , ARG C:32 , HOH C:366 , HOH C:382binding site for residue EDO C 205
14AD5SOFTWAREHIS C:114 , LEU C:115 , ASP C:116 , GLN C:117 , ARG C:121binding site for residue EDO C 206
15AD6SOFTWAREHIS A:65 , ARG A:66 , ASN D:49 , LYS D:50 , ARG D:51 , HOH D:333 , HOH D:341binding site for residue SO4 D 201
16AD7SOFTWAREARG A:70 , HOH A:308 , ARG D:32 , ARG D:33 , HOH D:308 , HOH D:318binding site for residue SO4 D 202
17AD8SOFTWAREARG A:66 , ARG D:51 , LYS D:54binding site for residue SO4 D 203
18AD9SOFTWARELYS A:73 , THR D:7 , HIS D:8 , THR D:11 , HOH D:326binding site for residue SO4 D 204
19AE1SOFTWAREGLY C:20 , ARG C:21 , ALA C:98 , HOH C:309 , ARG D:31 , GLY D:34 , HOH D:304 , HOH D:305 , HOH D:337 , HOH D:354 , HOH D:371binding site for residue PGE D 205

(-) SS Bonds  (12, 12)

Asymmetric Unit
No.Residues
1A:26 -A:81
2A:39 -A:92
3A:57 -A:107
4B:26 -B:81
5B:39 -B:92
6B:57 -B:107
7C:26 -C:81
8C:39 -C:92
9C:57 -C:107
10D:26 -D:81
11D:39 -D:92
12D:57 -D:107

(-) Cis Peptide Bonds  (8, 9)

Asymmetric Unit
No.Residues
1Ser A:37 -Pro A:38
2Pro A:90 -Pro A:91
3Ser B:37 -Pro B:38
4Pro B:90 -Pro B:91
5Ser C:37 -Pro C:38
6Pro C:90 -Pro C:91
7Ser D:37 -Pro D:38
8Pro D:90 -Pro D:91

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5M9M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5M9M)

(-) Exons   (0, 0)

(no "Exon" information available for 5M9M)

(-) 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 ------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhh.......hhhhhhhhhhhh........eeeee..hhhhhhhhhh...eeee...eeee...eeeeeeeee........eeeeeeeee..eeeee..eeeee.hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 5m9m A   3 NSRYTHFLTQHYDAKPQGRDDRYCESIMRRRGLTSPCKDINTFIHGNKRSIKAICENKNGNPHRENLRISKSSFPVTTCKLHGGSPWPPCQYRATAGFRNVVVACENGLPVHLDQSIFRR 122
                                    12        22        32        42        52        62        72        82        92       102       112       122


Chain B from PDB  Type:PROTEIN  Length:121
                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.......hhhhhhhhhhhh........eeeee..hhhhhhhhhh...eeee...eeee...eeeeeeeee........eeeeeeeee..eeeee..eeeee.hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 5m9m B   1 QDNSRYTHFLTQHYDAKPQGRDDRYCESIMRRRGLTSPCKDINTFIHGNKRSIKAICENKNGNPHRENLRISKSSFPVTTCKLHGGSPWPPCQYRATAGFRNVVVACENGLPVHLDQSIFR 121
                                    10        20        30        40        50        60        70        80        90       100       110       120 


Chain C from PDB  Type:PROTEIN  Length:116
                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.......hhhhhhhhhhhh........eeeee..hhhhhhhh..........ee....eeeeeeeee........eeeeeeeee..eeeee..eeeee.hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 5m9m C   3 NSRYTHFLTQHYDAKPQGRDDRYCESIMRRRGLTSPCKDINTFIHGNKRSIKAICENKNGNPNLRISKSSFPVTTCKLHGGSPWPPCQYRATAGFRNVVVACENGLPVHLDQSIFR 121
                                    12        22        32        42        52        62 ||     75        85        95       105       115      
                                                                                        64|                                                     
                                                                                         68                                                     


Chain D from PDB  Type:PROTEIN  Length:119
                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.......hhhhhhhhhhhh........eeeee..hhhhhhhhhh...eeee...eeee...eeeeeeeee........eeeeeeeee..eeeee..eeeee.hhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 5m9m D   3 NSRYTHFLTQHYDAKPQGRDDRYCESIMRRRGLTSPCKDINTFIHGNKRSIKAICENKNGNPHRENLRISKSSFPVTTCKLHGGSPWPPCQYRATAGFRNVVVACENGLPVHLDQSIFR 121
                                    12        22        32        42        52        62        72        82        92       102       112
   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 5M9M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5M9M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5M9M)

(-) Gene Ontology  (54, 54)

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  3.1.27.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        ANGI_HUMAN | P03950: 1a4y 1ang 1awz 1b1e 1b1i 1b1j 1gv7 1h0d 1h52 1h53 1hby 1k58 1k59 1k5a 1k5b 1un3 1un4 1un5 2ang 4ahd 4ahe 4ahf 4ahg 4ahh 4ahi 4ahj 4ahk 4ahl 4ahm 4ahn 4aoh 4b36 5eop 5epz 5eqo 5m9a 5m9c 5m9g 5m9j 5m9p 5m9q 5m9r 5m9s 5m9t 5m9v

(-) Related Entries Specified in the PDB File

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