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(-) Description

Title :  SPERM WHALE MYOGLOBIN H64A WITH NITROSOAMPHETAMINE
 
Authors :  B. Wang, Y. Guan, L. M. Thomas, G. B. Richter-Addo
Date :  07 Jun 16  (Deposition) - 10 May 17  (Release) - 17 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (3x)
Keywords :  Heme, Myoglobin, Nitrosoalkane, Nitrosoamphetamine, 2-Nitroso-1- Phenylpropane, N-Hydroxyamphetamine, C-Nitroso, Oxygen Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. Wang, S. M. Powell, Y. Guan, N. Xu, L. M. Thomas, G. B. Richter-Addo
Nitrosoamphetamine Binding To Myoglobin And Hemoglobin: Crystal Structure Of The H64A Myoglobin-Nitrosoamphetamine Adduct.
Nitric Oxide V. 67 26 2017
PubMed-ID: 28450187  |  Reference-DOI: 10.1016/J.NIOX.2017.04.012

(-) Compounds

Molecule 1 - MYOGLOBIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneMB
    MutationYES
    Organism CommonSPERM WHALE
    Organism ScientificPHYSETER CATODON
    Organism Taxid9755
    Other DetailsALA A 64 UNP P02185 HIS 65 ENGINEERED MUTATION ASN A 122 UNP P02185 ASP 123 VARIANT

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (1x)A
Biological Unit 2 (3x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric Unit (4, 11)
No.NameCountTypeFull Name
13QM1Ligand/Ion[(2R)-2-NITROSOPROPYL]BENZENE
2GOL5Ligand/IonGLYCEROL
3HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4SO44Ligand/IonSULFATE ION
Biological Unit 1 (4, 11)
No.NameCountTypeFull Name
13QM1Ligand/Ion[(2R)-2-NITROSOPROPYL]BENZENE
2GOL5Ligand/IonGLYCEROL
3HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4SO44Ligand/IonSULFATE ION
Biological Unit 2 (4, 33)
No.NameCountTypeFull Name
13QM3Ligand/Ion[(2R)-2-NITROSOPROPYL]BENZENE
2GOL15Ligand/IonGLYCEROL
3HEM3Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4SO412Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:42 , PHE A:43 , ARG A:45 , THR A:67 , VAL A:68 , LEU A:89 , SER A:92 , HIS A:93 , HIS A:97 , ILE A:99 , TYR A:103 , LEU A:104 , 3QM A:206 , HOH A:329 , HOH A:331 , HOH A:359 , HOH A:407binding site for residue HEM A 201
02AC2SOFTWARESER A:3 , GLU A:4 , THR A:51 , GLU A:52 , ALA A:53 , HOH A:308 , HOH A:344binding site for residue SO4 A 202
03AC3SOFTWAREALA A:15 , LYS A:16 , HOH A:437binding site for residue SO4 A 203
04AC4SOFTWARELYS A:87 , GLY A:124 , ALA A:125 , ASP A:126 , GOL A:209 , HOH A:301 , HOH A:433binding site for residue SO4 A 204
05AC5SOFTWARESER A:3 , GLY A:5 , HOH A:344 , HOH A:430 , HOH A:434binding site for residue SO4 A 205
06AC6SOFTWAREALA A:64 , VAL A:68 , HEM A:201binding site for residue 3QM A 206
07AC7SOFTWAREALA A:57 , SER A:58 , GLU A:59 , ASP A:60 , HOH A:311 , HOH A:321 , HOH A:364binding site for residue GOL A 207
08AC8SOFTWAREARG A:31 , LYS A:98 , HIS A:113binding site for residue GOL A 208
09AC9SOFTWAREGLY A:121 , ASN A:122 , PHE A:123 , GLY A:124 , ASP A:126 , ALA A:127 , SO4 A:204 , HOH A:348 , HOH A:353 , HOH A:379binding site for residue GOL A 209
10AD1SOFTWARELYS A:78 , HIS A:81 , HIS A:82 , GLU A:83 , ALA A:84 , GLU A:85 , GOL A:211 , HOH A:320 , HOH A:465binding site for residue GOL A 210
11AD2SOFTWAREHIS A:48 , HIS A:81 , GOL A:210 , HOH A:354binding site for residue GOL A 211

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5KD1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5KD1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5KD1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5KD1)

(-) Exons   (0, 0)

(no "Exon" information available for 5KD1)

(-) 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    
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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:153
                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kd1 A   1 VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASEDLKKAGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHPGNFGADAQGAMNKALELFRKDIAAKYKELGYQG 153
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150   

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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 5KD1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5KD1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5KD1)

(-) Gene Ontology  (6, 6)

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 Related Entries

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

UniProtKB/Swiss-Prot
        MYG_PHYCD | P02185101m 102m 103m 104m 105m 106m 107m 108m 109m 110m 111m 112m 1a6g 1a6k 1a6m 1a6n 1abs 1ajg 1ajh 1bvc 1bvd 1bz6 1bzp 1bzr 1ch1 1ch2 1ch3 1ch5 1ch7 1ch9 1cik 1cio 1co8 1co9 1cp0 1cp5 1cpw 1cq2 1do1 1do3 1do4 1do7 1dti 1dtm 1duk 1duo 1dxc 1dxd 1ebc 1f63 1f65 1f6h 1fcs 1h1x 1hjt 1iop 1irc 1j3f 1j52 1jdo 1jp6 1jp8 1jp9 1jpb 1jw8 1l2k 1ltw 1lue 1mbc 1mbd 1mbi 1mbn 1mbo 1mcy 1mgn 1mlf 1mlg 1mlh 1mlj 1mlk 1mll 1mlm 1mln 1mlo 1mlq 1mlr 1mls 1mlu 1moa 1mob 1moc 1mod 1mti 1mtj 1mtk 1myf 1mym 1myz 1mz0 1n9f 1n9h 1n9i 1n9x 1naz 1o16 1obm 1ofj 1ofk 1spe 1swm 1tes 1u7r 1u7s 1ufj 1ufp 1v9q 1vxa 1vxb 1vxc 1vxd 1vxe 1vxf 1vxg 1vxh 1wvp 1yog 1yoh 1yoi 2blh 2bli 2blj 2bw9 2bwh 2cmm 2d6c 2e2y 2eb8 2eb9 2ef2 2ekt 2eku 2evk 2evp 2g0r 2g0s 2g0v 2g0x 2g0z 2g10 2g11 2g12 2g14 2jho 2mb5 2mbw 2mga 2mgb 2mgc 2mgd 2mge 2mgf 2mgg 2mgh 2mgi 2mgj 2mgk 2mgl 2mgm 2mya 2myb 2myc 2myd 2mye 2oh8 2oh9 2oha 2ohb 2spl 2spm 2spn 2spo 2w6w 2w6x 2w6y 2z6s 2z6t 2zsn 2zso 2zsp 2zsq 2zsr 2zss 2zst 2zsx 2zsy 2zsz 2zt0 2zt1 2zt2 2zt3 2zt4 3a2g 3ase 3e4n 3e55 3e5i 3e5o 3ecl 3ecx 3ecz 3ed9 3eda 3edb 3h57 3h58 3k9z 3m38 3m39 3m3a 3m3b 3mn0 3nml 3o89 3ogb 3sdn 3u3e 4fwx 4fwy 4fwz 4h07 4h0b 4it8 4lpi 4mbn 4mxk 4mxl 4nxa 4nxc 4of9 4ood 4pnj 4pq6 4pqb 4pqc 4qau 4tyx 5b84 5b85 5c6y 5hav 5hlq 5hlu 5hlx 5iks 5ile 5ilm 5ilp 5ilr 5jom 5kkk 5m3r 5m3s 5mbn 5o41

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5KD1)