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(-) Description

Title :  CRYSTAL STRUCTURE OF AN ALTERNATING D-ALANYL, L-HOMOALANYL PNA
 
Authors :  J. A. Cuesta-Seijo, G. M. Sheldrick, J. Zhang, U. Diederichsen
Date :  23 Jan 08  (Deposition) - 27 Jan 09  (Release) - 26 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Synthetic, Peptide Nucleic Acid, Pna, Alanyl, Homoalanyl, De Novo Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. Cuesta-Seijo, J. Zhang, U. Diederichsen, G. M. Sheldrick
Continuous Beta-Turn Fold Of An Alternating Alanyl/Homoalanyl Peptide Nucleic Acid.
Acta Crystallogr. , Sect. D V. 68 1067 2012
PubMed-ID: 22868773  |  Reference-DOI: 10.1107/S090744491202118X

(-) Compounds

Molecule 1 - PEPTIDE NUCLEIC ACID DLY-HGL-AGD-LHC-AGD-LHC-CUD-LYS
    Chains: A, B, C, D
    Engineered: YES
    Other Details: SYNTHETIC
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 28)

Asymmetric/Biological Unit (5, 28)
No.NameCountTypeFull Name
1AGD8Mod. Amino Acid3-(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)-D-ALANINE
2CUD4Mod. Amino Acid3-(4-AMINO-2-OXOPYRIMIDIN-1(2H)-YL)-D-ALANINE
3DLY4Mod. Amino AcidD-LYSINE
4HGL4Mod. Amino Acid(2S)-2-AMINO-4-(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)BUTANOIC ACID
5LHC8Mod. Amino Acid(2S)-2-AMINO-4-(4-AMINO-2-OXOPYRIMIDIN-1(2H)-YL)BUTANOIC ACID

(-) Sites  (28, 28)

Asymmetric Unit (28, 28)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHGL A:12 , AGD A:13 , LHC A:14 , HOH A:75 , HOH A:130 , HGL D:42BINDING SITE FOR RESIDUE DLY A 11
02AC2SOFTWAREDLY A:11 , AGD A:13 , LHC A:14 , HOH A:55 , HOH A:87 , HOH A:196 , HOH A:200 , LHC B:26 , CUD B:27BINDING SITE FOR RESIDUE HGL A 12
03AC3SOFTWAREDLY A:11 , HGL A:12 , LHC A:14 , AGD A:15 , LHC A:16 , HOH A:64 , HOH A:112 , HOH A:145 , AGD B:23 , LHC B:26BINDING SITE FOR RESIDUE AGD A 13
04AC4SOFTWAREDLY A:11 , HGL A:12 , AGD A:13 , AGD A:15 , LHC A:16 , HOH A:51 , HOH A:111 , HOH A:132 , LHC C:34 , AGD C:35BINDING SITE FOR RESIDUE LHC A 14
05AC5SOFTWAREAGD A:13 , LHC A:14 , LHC A:16 , CUD A:17 , LYS A:18 , HOH A:65 , HOH A:69 , HOH A:76 , HOH A:114 , DLY C:31 , LHC C:34 , HOH C:86BINDING SITE FOR RESIDUE AGD A 15
06AC6SOFTWAREAGD A:13 , LHC A:14 , AGD A:15 , CUD A:17 , LYS A:18 , HOH A:84 , HOH A:102 , HOH A:122 , HOH A:172 , HGL B:22 , AGD B:23BINDING SITE FOR RESIDUE LHC A 16
07AC7SOFTWAREAGD A:15 , LHC A:16 , LYS A:18 , HOH A:117 , HOH A:129 , HOH A:163 , HGL B:22BINDING SITE FOR RESIDUE CUD A 17
08AC8SOFTWAREHGL B:22 , AGD B:23 , LHC B:24 , HOH B:160 , HOH B:185 , AGD D:45BINDING SITE FOR RESIDUE DLY B 21
09AC9SOFTWARELHC A:16 , CUD A:17 , DLY B:21 , AGD B:23 , LHC B:24 , HOH B:85 , HOH B:107BINDING SITE FOR RESIDUE HGL B 22
10BC1SOFTWAREAGD A:13 , LHC A:16 , DLY B:21 , HGL B:22 , LHC B:24 , AGD B:25 , LHC B:26 , HOH B:120 , HOH B:149BINDING SITE FOR RESIDUE AGD B 23
11BC2SOFTWAREDLY B:21 , HGL B:22 , AGD B:23 , AGD B:25 , LHC B:26 , HOH B:52 , HOH B:95 , HOH B:140 , LHC D:44 , AGD D:45BINDING SITE FOR RESIDUE LHC B 24
12BC3SOFTWAREAGD B:23 , LHC B:24 , LHC B:26 , CUD B:27 , HOH B:81 , HOH B:188 , LHC D:44BINDING SITE FOR RESIDUE AGD B 25
13BC4SOFTWAREHGL A:12 , AGD A:13 , AGD B:23 , LHC B:24 , AGD B:25 , CUD B:27 , HOH B:139 , HOH B:142 , HOH B:186BINDING SITE FOR RESIDUE LHC B 26
14BC5SOFTWAREHGL A:12 , AGD B:25 , LHC B:26 , LYS B:28 , HOH B:113BINDING SITE FOR RESIDUE CUD B 27
15BC6SOFTWAREAGD A:15 , HGL C:32 , AGD C:33 , LHC C:34 , HOH C:86 , HOH C:97BINDING SITE FOR RESIDUE DLY C 31
16BC7SOFTWAREDLY C:31 , AGD C:33 , LHC C:34 , HOH C:60 , HOH C:68 , HOH C:192 , LHC D:46 , CUD D:47BINDING SITE FOR RESIDUE HGL C 32
17BC8SOFTWAREDLY C:31 , HGL C:32 , LHC C:34 , AGD C:35 , LHC C:36 , HOH C:53 , HOH C:116 , HOH C:131 , HOH C:135 , HOH C:170 , AGD D:43 , LHC D:46BINDING SITE FOR RESIDUE AGD C 33
18BC9SOFTWARELHC A:14 , AGD A:15 , DLY C:31 , HGL C:32 , AGD C:33 , AGD C:35 , LHC C:36 , HOH C:72 , HOH C:79 , HOH C:106BINDING SITE FOR RESIDUE LHC C 34
19CC1SOFTWARELHC A:14 , AGD C:33 , LHC C:34 , LHC C:36 , CUD C:37 , LYS C:38 , HOH C:58 , HOH C:71 , HOH C:83 , HOH C:182BINDING SITE FOR RESIDUE AGD C 35
20CC2SOFTWAREAGD C:33 , LHC C:34 , AGD C:35 , CUD C:37 , LYS C:38 , HOH C:94 , HOH C:103 , HOH C:159 , HGL D:42 , AGD D:43BINDING SITE FOR RESIDUE LHC C 36
21CC3SOFTWAREAGD C:35 , LHC C:36 , LYS C:38 , HOH C:63 , HOH C:166 , HGL D:42 , HOH D:70BINDING SITE FOR RESIDUE CUD C 37
22CC4SOFTWAREHGL D:42 , AGD D:43 , LHC D:44 , HOH D:138BINDING SITE FOR RESIDUE DLY D 41
23CC5SOFTWAREDLY A:11 , LHC C:36 , CUD C:37 , DLY D:41 , AGD D:43 , LHC D:44 , HOH D:80 , HOH D:82 , HOH D:88 , HOH D:96 , HOH D:193BINDING SITE FOR RESIDUE HGL D 42
24CC6SOFTWAREAGD C:33 , LHC C:36 , HOH C:116 , DLY D:41 , HGL D:42 , LHC D:44 , AGD D:45 , LHC D:46 , HOH D:104 , HOH D:118 , HOH D:158 , HOH D:211BINDING SITE FOR RESIDUE AGD D 43
25CC7SOFTWARELHC B:24 , AGD B:25 , DLY D:41 , HGL D:42 , AGD D:43 , AGD D:45 , LHC D:46 , HOH D:78 , HOH D:128BINDING SITE FOR RESIDUE LHC D 44
26CC8SOFTWAREDLY B:21 , LHC B:24 , HOH B:185 , AGD D:43 , LHC D:44 , LHC D:46 , CUD D:47 , LYS D:48 , HOH D:57 , HOH D:62 , HOH D:99 , HOH D:108BINDING SITE FOR RESIDUE AGD D 45
27CC9SOFTWAREHGL C:32 , AGD C:33 , AGD D:43 , LHC D:44 , AGD D:45 , CUD D:47 , LYS D:48 , HOH D:74 , HOH D:91 , HOH D:98 , HOH D:105BINDING SITE FOR RESIDUE LHC D 46
28DC1SOFTWAREHGL C:32 , AGD D:45 , LHC D:46 , LYS D:48 , HOH D:77 , HOH D:126 , HOH D:169BINDING SITE FOR RESIDUE CUD D 47

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3C1P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3C1P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3C1P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3C1P)

(-) Exons   (0, 0)

(no "Exon" information available for 3C1P)

(-) Sequences/Alignments

Asymmetric/Biological 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:8
                                       
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                  3c1p A 11 xxxxxxxK 18
                            ||||||| 
                            ||||||| 
                           11-DLY|| 
                            12-HGL| 
                             13-AGD 
                              14-LHC
                               15-AGD
                                16-LHC
                                 17-CUD


Chain B from PDB  Type:PROTEIN  Length:8
                                       
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                  3c1p B 21 xxxxxxxK 28
                            ||||||| 
                            ||||||| 
                           21-DLY|| 
                            22-HGL| 
                             23-AGD 
                              24-LHC
                               25-AGD
                                26-LHC
                                 27-CUD


Chain C from PDB  Type:PROTEIN  Length:8
                                       
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                  3c1p C 31 xxxxxxxK 38
                            ||||||| 
                            ||||||| 
                           31-DLY|| 
                            32-HGL| 
                             33-AGD 
                              34-LHC
                               35-AGD
                                36-LHC
                                 37-CUD


Chain D from PDB  Type:PROTEIN  Length:8
                                       
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                  3c1p D 41 xxxxxxxK 48
                            ||||||| 
                            ||||||| 
                           41-DLY|| 
                            42-HGL| 
                             43-AGD 
                              44-LHC
                               45-AGD
                                46-LHC
                                 47-CUD
   Legend:   → Mismatch (orange background)
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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 3C1P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3C1P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3C1P)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
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