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Asym./Biol. Unit (Jmol Viewer)

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Title :   X RAY CRYSTAL STRUCTURE OF RABBIT HEMOGLOBIN (OXY FORM) AT 2.0 ANGSTROM RESOLUTION

Authors :   S. Sundaresan, C. Packianathan, K. Neelagandan, M. N. Ponnuswamy

Date :   17 Sep 07 (Deposition) - 09 Sep 08 (Release) - 14 Oct 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Oxygen Tranport/Storage, Heme, Iron, Metal-Binding, Oxygen Transport, Transport, Oxygen Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Sundaresan, C. Packianathan, K. Neelagandan, M. N. Ponnuswamy
X-Ray Crystal Structure Determination Of Hemoglobin From Rabbit At 2. 0 Angstrom Resloution
To Be Published
PubMed: search

Molecule 1 - HEMOGLOBIN SUBUNIT ALPHA-1/2
	Chains	:	A, C
	Organism Common	:	RABBIT
	Organism Scientific	:	ORYCTOLAGUS CUNICULUS
	Organism Taxid	:	9986
	Synonym	:	HEMOGLOBIN ALPHA SUBUNIT, HEMOGLOBIN ALPHA-1/2 CHAIN, ALPHA- 1/2-GLOBIN
	Tissue	:	RED BLOOD CELLS

Molecule 2 - HEMOGLOBIN SUBUNIT BETA-1/2
	Chains	:	B, D
	Organism Common	:	RABBIT
	Organism Scientific	:	ORYCTOLAGUS CUNICULUS
	Organism Taxid	:	9986
	Synonym	:	HEMOGLOBIN BETA SUBUNIT, HEMOGLOBIN BETA-1/2 CHAIN, BETA- 1/2-GLOBIN
	Tissue	:	RED BLOOD CELLS

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 8)

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

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:42 , PHE A:43 , HIS A:45 , HIS A:58 , LYS A:61 , LEU A:86 , HIS A:87 , LEU A:91 , VAL A:93 , ASN A:97 , PHE A:98 , LEU A:136 , OXY A:143 , HOH A:164 , HOH A:169 , HIS D:2	BINDING SITE FOR RESIDUE HEM A 142
2	AC2	SOFTWARE	HIS A:58 , HEM A:142	BINDING SITE FOR RESIDUE OXY A 143
3	AC3	SOFTWARE	THR B:38 , PHE B:41 , PHE B:42 , HIS B:63 , PHE B:71 , HIS B:92 , LEU B:96 , ASN B:102 , LEU B:106 , LEU B:141 , OXY B:148	BINDING SITE FOR RESIDUE HEM B 147
4	AC4	SOFTWARE	HIS B:63 , VAL B:67 , HEM B:147	BINDING SITE FOR RESIDUE OXY B 148
5	AC5	SOFTWARE	HIS C:58 , HEM C:142	BINDING SITE FOR RESIDUE OXY C 143
6	AC6	SOFTWARE	TYR C:42 , PHE C:43 , HIS C:45 , PHE C:46 , HIS C:58 , LYS C:61 , HIS C:87 , LEU C:91 , VAL C:93 , ASN C:97 , PHE C:98 , LEU C:136 , OXY C:143 , HOH C:159 , HOH C:193	BINDING SITE FOR RESIDUE HEM C 142
7	AC7	SOFTWARE	HIS D:63 , VAL D:67 , LEU D:106 , HEM D:147	BINDING SITE FOR RESIDUE OXY D 148
8	AC8	SOFTWARE	THR A:8 , LYS A:11 , PHE D:41 , PHE D:42 , HIS D:63 , LEU D:88 , HIS D:92 , LEU D:96 , ASN D:102 , OXY D:148 , HOH D:172	BINDING SITE FOR RESIDUE HEM D 147

(no "SS Bond" information available for 2RAO)

(no "Cis Peptide Bond" information available for 2RAO)

Asymmetric/Biological Unit (5, 10)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_HBA_RABIT_001 *	V	30	L	HBA_RABIT	---	---	A/C	V	29	L
2	UniProt	VAR_HBB_RABIT_001 *	N	53	H	HBB_RABIT	---	---	B/D	N	52	H
3	UniProt	VAR_HBB_RABIT_002 *	N	57	S	HBB_RABIT	---	---	B/D	N	56	S
4	UniProt	VAR_HBB_RABIT_003 *	S	77	N	HBB_RABIT	---	---	B/D	S	76	N
5	UniProt	VAR_HBB_RABIT_004 *	I	113	V	HBB_RABIT	---	---	B/D	I	112	V
	* 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.	HBB_RABIT	2-147	2	B:1-146 D:1-146
1	GLOBIN	PS01033	Globin family profile.	HBA_RABIT	3-142	2	A:2-141 C:2-141

(no "Exon" information available for 2RAO)

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_RABIT | P01948 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:141
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141 
            HBA_RABIT     2 VLSPADKTNIKTAWEKIGSHGGEYGAEAVERMFLGFPTTKTYFPHFDFTHGSEQIKAHGKKVSEALTKAVGHLDDLPGALSTLSDLHAHKLRVDPVNFKLLSHCLLVTLANHHPSEFTPAVHASLDKFLANVSTVLTSKYR 142
               SCOP domains d2raoa_ A: automated matches                                                                                                                  SCOP domains
               CATH domains 2raoA00 A:1-141 Globins                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------L---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -GLOBIN  PDB: A:2-141 UniProt: 3-142                                                                                                          PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rao A   1 VLSPADKTNIKTAWEKIGSHGGEYGAEAVERMFLGFPTTKTYFPHFDFTHGSEQIKAHGKKVSEALTKAVGHLDDLPGALSTLSDLHAHKLRVDPVNFKLLSHCLLVTLANHHPSEFTPAVHASLDKFLANVSTVLTSKYR 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_RABIT | P02057 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:146
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141      
            HBB_RABIT     2 VHLSSEEKSAVTALWGKVNVEEVGGEALGRLLVVYPWTQRFFESFGDLSSANAVMNNPKVKAHGKKVLAAFSEGLSHLDNLKGTFAKLSELHCDKLHVDPENFRLLGNVLVIVLSHHFGKEFTPQVQAAYQKVVAGVANALAHKYH 147
               SCOP domains d2raob_ B: automated matches                                                                                                                       SCOP domains
               CATH domains 2raoB00 B:1-146 Globins                                                                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------H---S-------------------N-----------------------------------V---------------------------------- SAPs(SNPs)
                    PROSITE GLOBIN  PDB: B:1-146 UniProt: 2-147                                                                                                                PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rao B   1 VHLSSEEKSAVTALWGKVNVEEVGGEALGRLLVVYPWTQRFFESFGDLSSANAVMNNPKVKAHGKKVLAAFSEGLSHLDNLKGTFAKLSELHCDKLHVDPENFRLLGNVLVIVLSHHFGKEFTPQVQAAYQKVVAGVANALAHKYH 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_RABIT | P01948 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:141
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141 
            HBA_RABIT     2 VLSPADKTNIKTAWEKIGSHGGEYGAEAVERMFLGFPTTKTYFPHFDFTHGSEQIKAHGKKVSEALTKAVGHLDDLPGALSTLSDLHAHKLRVDPVNFKLLSHCLLVTLANHHPSEFTPAVHASLDKFLANVSTVLTSKYR 142
               SCOP domains d2raoc_ C: automated matches                                                                                                                  SCOP domains
               CATH domains 2raoC00 C:1-141 Globins                                                                                                                       CATH domains
           Pfam domains (1) -----Globin-2raoC01 C:6-106                                                                               ----------------------------------- Pfam domains (1)
           Pfam domains (2) -----Globin-2raoC02 C:6-106                                                                               ----------------------------------- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------L---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -GLOBIN  PDB: C:2-141 UniProt: 3-142                                                                                                          PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rao C   1 VLSPADKTNIKTAWEKIGSHGGEYGAEAVERMFLGFPTTKTYFPHFDFTHGSEQIKAHGKKVSEALTKAVGHLDDLPGALSTLSDLHAHKLRVDPVNFKLLSHCLLVTLANHHPSEFTPAVHASLDKFLANVSTVLTSKYR 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_RABIT | P02057 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:146
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141      
            HBB_RABIT     2 VHLSSEEKSAVTALWGKVNVEEVGGEALGRLLVVYPWTQRFFESFGDLSSANAVMNNPKVKAHGKKVLAAFSEGLSHLDNLKGTFAKLSELHCDKLHVDPENFRLLGNVLVIVLSHHFGKEFTPQVQAAYQKVVAGVANALAHKYH 147
               SCOP domains d2raod_ D: automated matches                                                                                                                       SCOP domains
               CATH domains 2raoD00 D:1-146 Globins                                                                                                                            CATH domains
           Pfam domains (1) ------Globin-2raoD01 D:7-111                                                                                   ----------------------------------- Pfam domains (1)
           Pfam domains (2) ------Globin-2raoD02 D:7-111                                                                                   ----------------------------------- Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------H---S-------------------N-----------------------------------V---------------------------------- SAPs(SNPs)
                    PROSITE GLOBIN  PDB: D:1-146 UniProt: 2-147                                                                                                                PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rao D   1 VHLSSEEKSAVTALWGKVNVEEVGGEALGRLLVVYPWTQRFFESFGDLSSANAVMNNPKVKAHGKKVLAAFSEGLSHLDNLKGTFAKLSELHCDKLHVDPENFRLLGNVLVIVLSHHFGKEFTPQVQAAYQKVVAGVANALAHKYH 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)
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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 '\|'

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: automated matches (99)

Rabbit (Oryctolagus cuniculus) [TaxId: 9986] (1)

1a	d2raoa_	A:
1b	d2raob_	B:
1c	d2raoc_	C:
1d	d2raod_	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)

Rabbit (Oryctolagus cuniculus) (1)

1a	2raoB00	B:1-146
1b	2raoD00	D:1-146
1c	2raoA00	A:1-141
1d	2raoC00	C:1-141

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Globin (291)

Family: Globin (264)

Oryctolagus cuniculus (Rabbit) (1)

1a	Globin-2raoC01	C:6-106
1b	Globin-2raoC02	C:6-106
1c	Globin-2raoD01	D:7-111
1d	Globin-2raoD02	D:7-111

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,C (HBA_RABIT | P01948)

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.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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:0006417	regulation of translation	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
	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_RABIT | P02057)

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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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2rao)

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Ligands, Modified Residues, Ions (2, 8)

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SS Bonds (0, 0)

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