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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN ALPHA-DEFENSIN 5, HD5 (THR7ARG GLU21ARG MUTANT)
 
Authors :  M. Pazgier, N. Gohain, W. D. Tolbert
Date :  13 Sep 14  (Deposition) - 29 Jul 15  (Release) - 29 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Mutant T7R E21R-Hd5, Beta-Sheet, Antimicrobial Peptide, Paneth Cells Defensin, Human Alpha-Defensin, Antimicrobial Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Wang, M. Shen, N. Gohain, W. D. Tolbert, F. Chen, N. Zhang, K. Yang, A. Wang, Y. Su, T. Cheng, J. Zhao, M. Pazgier, J. Wang
Design Of A Potent Antibiotic Peptide Based On The Active Region Of Human Defensin 5.
J. Med. Chem. V. 58 3083 2015
PubMed-ID: 25782105  |  Reference-DOI: 10.1021/JM501824A

(-) Compounds

Molecule 1 - DEFENSIN-5
    Chains: A, B, C, D
    Engineered: YES
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HD5(63-94)
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A  D
Biological Unit 2 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric Unit (2, 11)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2SO49Ligand/IonSULFATE ION
Biological Unit 1 (1, 5)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2SO45Ligand/IonSULFATE ION
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2SO44Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:6 , ARG A:7 , GLY A:8 , HOH A:201 , HOH A:203 , HOH B:218BINDING SITE FOR RESIDUE SO4 A 101
02AC2SOFTWARETYR A:4 , GLY A:8 , ARG A:9 , ARG A:28 , ALA B:11 , THR B:12 , HOH B:217 , ARG D:21BINDING SITE FOR RESIDUE SO4 A 102
03AC3SOFTWAREARG A:7 , ARG A:25 , ARG B:13 , ARG D:21 , GLY D:24 , ARG D:25BINDING SITE FOR RESIDUE SO4 A 103
04AC4SOFTWAREARG A:13 , ARG A:32 , ARG B:6 , ARG B:7 , GLY B:8 , HOH B:202 , HOH B:219 , HOH B:222BINDING SITE FOR RESIDUE SO4 B 101
05AC5SOFTWAREALA A:11 , THR A:12 , TYR B:4 , GLY B:8 , ARG B:9 , ARG B:28 , HOH B:211 , ARG C:21BINDING SITE FOR RESIDUE SO4 B 102
06AC6SOFTWAREARG B:21 , ARG D:9BINDING SITE FOR RESIDUE CL B 103
07AC7SOFTWAREILE B:22 , SER B:23 , HOH B:207 , ARG C:7 , TYR C:27 , HOH C:208 , ALA D:11 , THR D:12 , HOH D:205BINDING SITE FOR RESIDUE SO4 C 101
08AC8SOFTWAREARG A:13 , ARG B:7 , ARG B:25 , ARG C:21 , GLY C:24 , ARG C:25 , HOH C:216BINDING SITE FOR RESIDUE SO4 C 102
09AC9SOFTWARETYR C:4BINDING SITE FOR RESIDUE CL C 103
10BC1SOFTWAREARG B:21 , HOH B:210 , HOH B:214 , ARG C:6 , ARG C:9 , ARG D:6 , ARG D:7 , GLY D:8 , HOH D:209 , HOH D:214BINDING SITE FOR RESIDUE SO4 D 101
11BC2SOFTWAREARG A:21 , GLY C:8 , ARG C:9 , ARG D:9 , ARG D:28 , HOH D:202BINDING SITE FOR RESIDUE SO4 D 102

(-) SS Bonds  (12, 12)

Asymmetric Unit
No.Residues
1A:3 -A:31
2A:5 -A:20
3A:10 -A:30
4B:3 -B:31
5B:5 -B:20
6B:10 -B:30
7C:3 -C:31
8C:5 -C:20
9C:10 -C:30
10D:3 -D:31
11D:5 -D:20
12D:10 -D:30

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RBW)

(-) 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:32
                                                               
               SCOP domains -------------------------------- SCOP domains
               CATH domains -------------------------------- CATH domains
               Pfam domains -------------------------------- Pfam domains
         Sec.struct. author .eeeee........eeeeeeee..eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------- PROSITE
                 Transcript -------------------------------- Transcript
                  4rbw A  1 ATCYCRRGRCATRESLSGVCRISGRLYRLCCR 32
                                    10        20        30  


Chain B from PDB  Type:PROTEIN  Length:32
                                                               
               SCOP domains -------------------------------- SCOP domains
               CATH domains -------------------------------- CATH domains
               Pfam domains -------------------------------- Pfam domains
         Sec.struct. author .eeeee........eeeeeeee..eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------- PROSITE
                 Transcript -------------------------------- Transcript
                  4rbw B  1 ATCYCRRGRCATRESLSGVCRISGRLYRLCCR 32
                                    10        20        30  


Chain C from PDB  Type:PROTEIN  Length:32
                                                               
               SCOP domains -------------------------------- SCOP domains
               CATH domains -------------------------------- CATH domains
               Pfam domains -------------------------------- Pfam domains
         Sec.struct. author ..eeee........eeeeeeee..eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------- PROSITE
                 Transcript -------------------------------- Transcript
                  4rbw C  1 ATCYCRRGRCATRESLSGVCRISGRLYRLCCR 32
                                    10        20        30  


Chain D from PDB  Type:PROTEIN  Length:32
                                                               
               SCOP domains -------------------------------- SCOP domains
               CATH domains -------------------------------- CATH domains
               Pfam domains -------------------------------- Pfam domains
         Sec.struct. author ..eeee........eeeeeeee..eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------- PROSITE
                 Transcript -------------------------------- Transcript
                  4rbw D  1 ATCYCRRGRCATRESLSGVCRISGRLYRLCCR 32
                                    10        20        30
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 4RBW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

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  4rbw
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  DEF5_HUMAN | Q01523
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 Related Entries

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

UniProtKB/Swiss-Prot
        DEF5_HUMAN | Q01523: 1zmp 2lxz 2mit 3i5w 4e82 4e83 4e86 4rbx 5cui 5cuj 5cum

(-) Related Entries Specified in the PDB File

1zmp CRYSTAL STRUCTURE OF HUMAN DEFENSIN 5
4e82 CRYSTAL STRUCTURE OF MONOMERIC VARIANT OF HUMAN ALPHA- DEFENSIN 5, HD5 (GLU21EME MUTANT)
4e83 CRYSTAL STRUCTURE OF HUMAN ALPHA-DEFENSIN 5, HD5 (LEU29NLE MUTANT)
4e86 CRYSTAL STRUCTURE OF HUMAN ALPHA-DEFENSIN 5, HD5 (LEU29ABA MUTANT)
4rbx