1Y8H - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   HORSE METHEMOGLOBIN LOW SALT, PH 7.0

Authors :   R. Sankaranarayanan, B. K. Biswal, M. Vijayan

Date :   13 Dec 04 (Deposition) - 26 Jul 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.10

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Aquo Methemoglobin, Quarternary Association, Allosteric Transition, Oxygen Storage/Transport Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Sankaranarayanan, B. K. Biswal, M. Vijayan
A New Relaxed State In Horse Methemoglobin Characterized By Crystallographic Studies.
Proteins V. 60 547 2005
PubMed-ID: 15887226 | Reference-DOI: 10.1002/PROT.20510
(for further references see the PDB file header)

Molecule 1 - HEMOGLOBIN ALPHA CHAINS
	Chains	:	A, C
	Organism Common	:	HORSE
	Organism Scientific	:	EQUUS CABALLUS
	Organism Taxid	:	9796
	Other Details	:	PH 7.0 AQUOMET STRUCTURE
	Synonym	:	SLOW AND FAST

Molecule 2 - HEMOGLOBIN BETA CHAIN
	Chains	:	B, D
	Organism Common	:	HORSE
	Organism Scientific	:	EQUUS CABALLUS
	Organism Taxid	:	9796

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 4)

No.	Name	Count	Type	Full Name
1	HEM	4	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:42 , HIS A:45 , HIS A:58 , LYS A:61 , HIS A:87 , VAL A:93 , PHE A:98 , HOH A:900	BINDING SITE FOR RESIDUE HEM A 142
2	AC2	SOFTWARE	LYS A:90 , PHE B:41 , PHE B:42 , HIS B:63 , HIS B:92 , LEU B:96 , VAL B:98 , ASN B:102 , PHE B:103 , LEU B:106 , LEU B:141 , HOH B:259 , HOH B:901	BINDING SITE FOR RESIDUE HEM B 147
3	AC3	SOFTWARE	TYR C:42 , HIS C:45 , HIS C:58 , LYS C:61 , HIS C:87 , VAL C:93 , PHE C:98	BINDING SITE FOR RESIDUE HEM C 142
4	AC4	SOFTWARE	LYS C:11 , PHE D:41 , PHE D:42 , HIS D:63 , HIS D:92 , LEU D:96 , VAL D:98 , ASN D:102 , PHE D:103 , LEU D:106 , LEU D:141 , HOH D:208 , HOH D:903	BINDING SITE FOR RESIDUE HEM D 147

(no "SS Bond" information available for 1Y8H)

(no "Cis Peptide Bond" information available for 1Y8H)

Asymmetric/Biological Unit (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_HBA_HORSE_001 *	Y	25	F	HBA_HORSE	---	---	A/C	Y	24	F
2	UniProt	VAR_HBA_HORSE_002 *	K	61	Q	HBA_HORSE	---	---	A/C	K	60	Q
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLOBIN	PS01033	Globin family profile.	HBA_HORSE	3-142	2	A:2-141 C:2-141
1	GLOBIN	PS01033	Globin family profile.	HBB_HORSE	3-146	2	B:3-146 D:3-146

(no "Exon" information available for 1Y8H)

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:141
 aligned with HBA_HORSE | P01958 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:141
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141 
            HBA_HORSE     2 VLSAADKTNVKAAWSKVGGHAGEYGAEALERMFLGFPTTKTYFPHFDLSHGSAQVKAHGKKVGDALTLAVGHLDDLPGALSNLSDLHAHKLRVDPVNFKLLSHCLLSTLAVHLPNDFTPAVHASLDKFLSSVSTVLTSKYR 142
               SCOP domains d1y8ha_ A: Hemoglobin, alpha-chain                                                                                                            SCOP domains
               CATH domains 1y8hA00 A:1-141 Globins                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -----------------------F-----------------------------------Q--------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -GLOBIN  PDB: A:2-141 UniProt: 3-142                                                                                                          PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y8h A   1 VLSAADKTNVKAAWSKVGGHAGEYGAEALERMFLGFPTTKTYFPHFDLSHGSAQVKAHGKKVGDALTLAVGHLDDLPGALSDLSNLHAHKLRVDPVNFKLLSHCLLSTLAVHLPNDFTPAVHASLDKFLSSVSTVLTSKYR 141
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain B from PDB  Type:PROTEIN  Length:146
 aligned with HBB_HORSE | P02062 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      
            HBB_HORSE     1 VQLSGEEKAAVLALWDKVNEEEVGGEALGRLLVVYPWTQRFFDSFGDLSNPGAVMGNPKVKAHGKKVLHSFGEGVHHLDNLKGTFAALSELHCDKLHVDPENFRLLGNVLVVVLARHFGKDFTPELQASYQKVVAGVANALAHKYH 146
               SCOP domains d1y8hb_ B: Hemoglobin, beta-chain                                                                                                                  SCOP domains
               CATH domains 1y8hB00 B:1-146 Globins                                                                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --GLOBIN  PDB: B:3-146 UniProt: 3-146                                                                                                              PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y8h B   1 VQLSGEEKAAVLALWDKVNEEEVGGEALGRLLVVYPWTQRFFDSFGDLSNPGAVMGNPKVKAHGKKVLHSFGEGVHHLDNLKGTFAALSELHCDKLHVDPENFRLLGNVLVVVLARHFGKDFTPELQASYQKVVAGVANALAHKYH 146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain C from PDB  Type:PROTEIN  Length:141
 aligned with HBA_HORSE | P01958 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:141
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141 
            HBA_HORSE     2 VLSAADKTNVKAAWSKVGGHAGEYGAEALERMFLGFPTTKTYFPHFDLSHGSAQVKAHGKKVGDALTLAVGHLDDLPGALSNLSDLHAHKLRVDPVNFKLLSHCLLSTLAVHLPNDFTPAVHASLDKFLSSVSTVLTSKYR 142
               SCOP domains d1y8hc_ C: Hemoglobin, alpha-chain                                                                                                            SCOP domains
               CATH domains 1y8hC00 C:1-141 Globins                                                                                                                       CATH domains
           Pfam domains (1) -----Globin-1y8hC01 C:6-106                                                                               ----------------------------------- Pfam domains (1)
           Pfam domains (2) -----Globin-1y8hC02 C:6-106                                                                               ----------------------------------- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -----------------------F-----------------------------------Q--------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -GLOBIN  PDB: C:2-141 UniProt: 3-142                                                                                                          PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y8h C   1 VLSAADKTNVKAAWSKVGGHAGEYGAEALERMFLGFPTTKTYFPHFDLSHGSAQVKAHGKKVGDALTLAVGHLDDLPGALSDLSNLHAHKLRVDPVNFKLLSHCLLSTLAVHLPNDFTPAVHASLDKFLSSVSTVLTSKYR 141
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain D from PDB  Type:PROTEIN  Length:146
 aligned with HBB_HORSE | P02062 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      
            HBB_HORSE     1 VQLSGEEKAAVLALWDKVNEEEVGGEALGRLLVVYPWTQRFFDSFGDLSNPGAVMGNPKVKAHGKKVLHSFGEGVHHLDNLKGTFAALSELHCDKLHVDPENFRLLGNVLVVVLARHFGKDFTPELQASYQKVVAGVANALAHKYH 146
               SCOP domains d1y8hd_ D: Hemoglobin, beta-chain                                                                                                                  SCOP domains
               CATH domains 1y8hD00 D:1-146 Globins                                                                                                                            CATH domains
           Pfam domains (1) ------Globin-1y8hD01 D:7-111                                                                                   ----------------------------------- Pfam domains (1)
           Pfam domains (2) ------Globin-1y8hD02 D:7-111                                                                                   ----------------------------------- Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --GLOBIN  PDB: D:3-146 UniProt: 3-146                                                                                                              PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y8h D   1 VQLSGEEKAAVLALWDKVNEEEVGGEALGRLLVVYPWTQRFFDSFGDLSNPGAVMGNPKVKAHGKKVLHSFGEGVHHLDNLKGTFAALSELHCDKLHVDPENFRLLGNVLVVVLARHFGKDFTPELQASYQKVVAGVANALAHKYH 146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Globin-like (1351)

Superfamily: Globin-like (1308)

Family: Globins (1157)

Protein domain: Hemoglobin, alpha-chain (292)

Horse (Equus caballus) [TaxId: 9796] (16)

1a	d1y8ha_	A:
1b	d1y8hc_	C:

Protein domain: Hemoglobin, beta-chain (292)

Horse (Equus caballus) [TaxId: 9796] (16)

2a	d1y8hb_	B:
2b	d1y8hd_	D:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Globin-like (786)

Homologous Superfamily: Globins (743)

Horse (Equus caballus) (63)

1a	1y8hB00	B:1-146
1b	1y8hD00	D:1-146
1c	1y8hA00	A:1-141
1d	1y8hC00	C:1-141

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Globin (291)

Family: Globin (264)

Equus caballus (Horse) (45)

1a	Globin-1y8hC01	C:6-106
1b	Globin-1y8hC02	C:6-106
1c	Globin-1y8hD01	D:7-111
1d	Globin-1y8hD02	D:7-111

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,C (HBA_HORSE | P01958)

molecular function
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	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: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: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:0005833	hemoglobin complex	An iron-containing, oxygen carrying complex. In vertebrates it is made up of two pairs of associated globin polypeptide chains, each chain carrying a noncovalently bound heme prosthetic group.

Chain B,D (HBB_HORSE | P02062)

molecular function
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	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: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: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:0005833	hemoglobin complex	An iron-containing, oxygen carrying complex. In vertebrates it is made up of two pairs of associated globin polypeptide chains, each chain carrying a noncovalently bound heme prosthetic group.

Asymmetric/Biological Unit
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	1y8h
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1jy7	STRUCTURE OF HUMAN METHAEMOGLOBIN: THE VARIATION OF A THEME. B.K.BISWAL, M.VIJAYAN, CURR.SCI.(INDIA), V.81, 1100, 2001
1lfq	STRUCTURES OF HUMAN OXY- AND DEOXYHAEMOGLOBIN AT DIFFERENT LEVELS OF HUMIDITY: VARIABILITY IN THE T STATE. ACTA CRYST., V.D58, 1155, 2002
1y8i
1y8k

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 4)

PROSITE Motifs (1, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 4)

CATH Domains (1, 4)

Pfam Domains (1, 4)

Gene Ontology (8, 16)

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