2VLX - JenaLib

Title :   CRYSTAL STRUCTURE OF PEROXYMYOGLOBIN GENERATED BY CRYORADIOLYTIC REDUCTION OF MYOGLOBIN COMPOUND III

Authors :   H. -P. Hersleth, C. H. Gorbitz, K. K. Andersson

Date :   20 Jan 08 (Deposition) - 10 Feb 09 (Release) - 08 Jun 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.30

Chains :   Asym./Biol. Unit : A

Keywords :   Haem, Iron, Heme, Ferryl, Transport, Peroxidase, Oxygen Transport, Oxygen Activation, Radiolytic- Reduction, Reaction Intermediate, Monooxygenase, Metal-Binding, Muscle Protein, X-Ray-Induced-Photoreduction (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. -P. Hersleth, Y. -W. Hsiao, U. Ryde, C. H. Gorbitz, K. K. Andersson
The Crystal Structure Of Peroxymyoglobin Generated Through Cryoradiolytic Reduction Of Myoglobin Compound Iii During Data Collection.
Biochem. J. V. 412 257 2008
PubMed-ID: 18215120 | Reference-DOI: 10.1042/BJ20070921
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 9)

Sites (9, 9)

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:39 , LYS A:42 , PHE A:43 , LYS A:45 , VAL A:68 , LEU A:89 , SER A:92 , HIS A:93 , HIS A:97 , ILE A:99 , TYR A:103 , LEU A:104 , HIS A:113 , HIS A:116 , GLN A:128 , PHE A:138 , PER A:1155 , HOH A:2161 , HOH A:2162 , HOH A:2163 , HOH A:2164 , HOH A:2165 , HOH A:2166	BINDING SITE FOR RESIDUE HEM A1154
2	AC2	SOFTWARE	PHE A:43 , HIS A:64 , VAL A:68 , HEM A:1154	BINDING SITE FOR RESIDUE PER A1155
3	AC3	SOFTWARE	THR A:51 , GLU A:52 , HOH A:2168 , HOH A:2169	BINDING SITE FOR RESIDUE SO4 A1156
4	AC4	SOFTWARE	HIS A:81 , HIS A:82 , GLU A:83 , HOH A:2170 , HOH A:2171	BINDING SITE FOR RESIDUE SO4 A1157
5	AC5	SOFTWARE	SER A:3 , ASP A:4 , GLY A:5 , HOH A:2172 , HOH A:2173	BINDING SITE FOR RESIDUE GOL A1158
6	AC6	SOFTWARE	ALA A:143 , TYR A:146 , LYS A:147 , PHE A:151 , GLN A:152 , HOH A:2159 , HOH A:2174	BINDING SITE FOR RESIDUE GOL A1159
7	AC7	SOFTWARE	GLY A:1 , LEU A:2 , TRP A:7 , HOH A:2175	BINDING SITE FOR RESIDUE PEO A1160
8	AC8	SOFTWARE	LYS A:147 , HOH A:2176	BINDING SITE FOR RESIDUE PEO A1161
9	AC9	SOFTWARE	GLU A:38 , GLU A:41 , LYS A:42 , LYS A:77 , TYR A:103 , HOH A:2087 , HOH A:2177	BINDING SITE FOR RESIDUE PEO A1162

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

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

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Chain A from PDB  Type:PROTEIN  Length:153
 aligned with MYG_HORSE | P68082 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:153
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151   
            MYG_HORSE     2 GLSDGEWQQVLNVWGKVEADIAGHGQEVLIRLFTGHPETLEKFDKFKHLKTEAEMKASEDLKKHGTVVLTALGGILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHSKHPGDFGADAQGAMTKALELFRNDIAAKYKELGFQG 154
               SCOP domains d2vlxa_ A: Myoglobin                                                                                                                                      SCOP domains
               CATH domains 2vlxA00 A:1-153 Globins                                                                                                                                   CATH domains
               Pfam domains -----Globin-2vlxA01 A:6-112                                                                                     ----------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -GLOBIN  PDB: A:2-147 UniProt: 3-148                                                                                                               ------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vlx A   1 GLSDGEWQQVLNVWGKVEADIAGHGQEVLIRLFTGHPETLEKFDKFKHLKTEAEMKASEDLKKHGTVVLTALGGILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHSKHPGDFGADAQGAMTKALELFRNDIAAKYKELGFQG 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 (1, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (MYG_HORSE | P68082)

molecular function
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0019825	oxygen binding	Interacting selectively and non-covalently with oxygen (O2).
	GO:0005344	oxygen transporter activity	Enables the directed movement of oxygen into, out of or within a cell, or between cells.
biological process
	GO:0050873	brown fat cell differentiation	The process in which a relatively unspecialized cell acquires specialized features of a brown adipocyte, an animal connective tissue cell involved in adaptive thermogenesis. Brown adipocytes contain multiple small droplets of triglycerides and a high number of mitochondria.
	GO:0043353	enucleate erythrocyte differentiation	The process in which a myeloid precursor cell acquires specialized features of an erythrocyte without a nucleus. An example of this process is found in Mus musculus.
	GO:0007507	heart development	The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
	GO:0015671	oxygen transport	The directed movement of oxygen (O2) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0001666	response to hypoxia	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File

1azi	MYOGLOBIN (HORSE HEART) RECOMBINANT WILD-TYPE COMPLEXED WITH AZIDE
1bje	H64T VARIANT OF MYOGLOBIN (HORSE HEART) RECOMBINANT WILD- TYPE COMPLEXED WITH AZIDE
1dwr	MYOGLOBIN (HORSE HEART) WILD-TYPE COMPLEXED WITH CO
1dws	MYOGLOBIN (HORSE HEART) WILD-TYPE COMPLEXED WITH CO
1dwt	PHOTORELAXED HORSE HEART MYOGLOBIN CO COMPLEX
1gjn	HYDROGEN PEROXIDE DERIVED MYOGLOBIN COMPOUND II AT PH 5.2
1hrm	MYOGLOBIN MUTANT WITH HIS 93 REPLACED BY TYR (H93Y)
1hsy	MYOGLOBIN MUTANT WITH HIS 64 REPLACED BY THR (H64T)
1npf	MYOGLOBIN (HORSE HEART) WILD-TYPE COMPLEXED WITH NITRICOXIDE
1npg	MYOGLOBIN (HORSE HEART) WILD-TYPE COMPLEXED WITHNITROSOETHANE
1nz2	K45E VARIANT OF HORSE HEART MYOGLOBIN
1nz3	K45E-K63E VARIANT OF HORSE HEART MYOGLOBIN
1nz4	THE HORSE HEART MYOGLOBIN VARIANT K45E/K63E COMPLEXED WITHCADMIUM
1nz5	THE HORSE HEART MYOGLOBIN VARIANT K45E/K63E COMPLEXED WITHMANGANESE
1rse	MYOGLOBIN (HORSE HEART) MUTANT WITH SER 92 REPLACED BY ASP (S92D)
1wla	MYOGLOBIN (HORSE HEART) RECOMBINANT WILD-TYPE
1xch	MYOGLOBIN (HORSE HEART) MUTANT WITH LEU 104 REPLACED BY ASN (L104N)
1yma	MYOGLOBIN (HORSE HEART) MUTANT WITH HIS 64 REPLACED BY TYR (H64Y)
1ymb	METMYOGLOBIN (HORSE HEART)
1ymc	CYANOMET-SULFMYOGLOBIN (HORSE HEART)
2frf	HORSE HEART MYOGLOBIN, NITRITE ADDUCT, CRYSTAL SOAK
2fri	HORSE HEART MYOGLOBIN, NITRITE ADDUCT, CO- CRYSTALLIZED
2frj	NITROSYL HORSE HEART MYOGLOBIN, NITRITE/ DITHIONITE METHOD
2frk	NITROSYL HORSE HEART MYOGLOBIN, NITRIC OXIDE GAS METHOD
2in4	CRYSTAL STRUCTURE OF MYOGLOBIN WITH CHARGE NEUTRALIZED HEME, ZNDMB-DME
2v1e	CRYSTAL STRUCTURE OF RADIATION-INDUCED MYOGLOBIN COMPOUND II - INTERMEDIATE H AT PH 6.8
2v1f	CRYSTAL STRUCTURE OF RADIATION-INDUCED MYOGLOBIN COMPOUND II - INTERMEDIATE H AT PH 8.7
2v1g	CRYSTAL STRUCTURE OF RADIATION-INDUCED MYOGLOBIN COMPOUND II - INTERMEDIATE H AT PH 5.2
2v1h	CRYSTAL STRUCTURE OF RADIATION-INDUCED METMYOGLOBIN - AQUA FERROUS MYOGLOBIN AT PH 5.2
2v1i	CRYSTAL STRUCTURE OF RADIATION-INDUCED METMYOGLOBIN - AQUA FERROUS MYOGLOBIN AT PH 6.8
2v1j	CRYSTAL STRUCTURE OF RADIATION-INDUCED METMYOGLOBIN - AQUA FERROUS MYOGLOBIN AT PH 8.7
2v1k	CRYSTAL STRUCTURE OF FERROUS DEOXYMYOGLOBIN AT PH 6.8
2vly	CRYSTAL STRUCTURE OF MYOGLOBIN COMPOUND III ( RADIATION- INDUCED)
2vlz	CRYSTAL STRUCTURE OF PEROXYMYOGLOBIN GENERATED BY CRYORADIOLYTIC REDUCTION OF MYOGLOBIN COMPOUND III
2vm0	CRYSTAL STRUCTURE OF RADIATION-INDUCED MYOGLOBIN COMPOUND II GENERATED AFTER ANNEALING OF PEROXYMYOGLOBIN

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