3CY5 - JenaLib

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Title :   CRYSTAL STRUCTURE DETERMINATION OF BUFFALO (BUBALUS BUBALIS) HEMOGLOBIN AT 2 ANGSTROM RESOLUTION

Authors :   M. Balasubramanian, P. Sathya Moorthy, K. Neelagandan, M. N. Ponnusw

Date :   25 Apr 08 (Deposition) - 28 Apr 09 (Release) - 21 Dec 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D  (1x)
Biol. Unit 2: A,B  (1x)
Biol. Unit 3: C,D  (1x)

Keywords :   Bb Phenotype, Bubalus Bubalis, Low Oxygen-Affinity, Orthorhombic, Methemoglobin, Heme, Iron, Transport, Oxygen Storage, Oxygen Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Balasubramanian, P. Sathya Moorthy, K. Neelagandan, M. N. Ponnuswamy
Crystal Structure Determination Of Hemoglobin From Buffalo (Bubalus Bubalis) At 2 Angstrom Resolution
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - HEMOGLOBIN SUBUNIT ALPHA-2
	Cell	:	RED BLOOD CELLS (RBC)
	Chains	:	A, C
	Organism Common	:	DOMESTIC WATER BUFFALO
	Organism Scientific	:	BUBALUS BUBALIS
	Organism Taxid	:	89462
	Synonym	:	HEMOGLOBIN ALPHA-2 CHAIN, ALPHA-2-GLOBIN, IALPHA2
	Tissue	:	BLOOD

Molecule 2 - HEMOGLOBIN SUBUNIT BETA
	Cell	:	RED BLOOD CELLS (RBC)
	Chains	:	B, D
	Organism Common	:	DOMESTIC WATER BUFFALO
	Organism Scientific	:	BUBALUS BUBALIS
	Organism Taxid	:	89462
	Synonym	:	HEMOGLOBIN BETA CHAIN, BETA-GLOBIN
	Tissue	:	BLOOD

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B	C	D
Biological Unit 2 (1x)	:	A	B
Biological Unit 3 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

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

Biological Unit 1 (1, 4)

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

Biological Unit 2 (1, 2)

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

Biological Unit 3 (1, 2)

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

Asymmetric Unit (4, 4)

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:83 , HIS A:87 , LEU A:91 , VAL A:93 , ASN A:97 , PHE A:98 , LEU A:101 , LEU A:136 , HOH A:154 , HOH A:200	BINDING SITE FOR RESIDUE HEM A 142
2	AC2	SOFTWARE	ALA A:4 , THR B:38 , PHE B:41 , PHE B:42 , HIS B:63 , LYS B:66 , SER B:70 , LEU B:88 , HIS B:92 , LEU B:96 , ASN B:102 , PHE B:103 , LEU B:106 , LEU B:141 , HOH B:165 , HOH B:174	BINDING SITE FOR RESIDUE HEM B 147
3	AC3	SOFTWARE	TYR C:42 , PHE C:43 , HIS C:45 , HIS C:58 , LYS C:61 , LEU C:83 , LEU C:86 , HIS C:87 , LEU C:91 , VAL C:93 , ASN C:97 , PHE C:98 , LEU C:101 , LEU C:136 , HOH C:169 , HOH C:206	BINDING SITE FOR RESIDUE HEM C 142
4	AC4	SOFTWARE	LYS B:8 , THR D:38 , PHE D:41 , PHE D:42 , HIS D:63 , LYS D:66 , SER D:70 , PHE D:71 , LEU D:88 , HIS D:92 , ASN D:102 , LEU D:106 , LEU D:141 , HOH D:167	BINDING SITE FOR RESIDUE HEM D 147

(no "SS Bond" information available for 3CY5)

(no "Cis Peptide Bond" information available for 3CY5)

(no "SAP(SNP)/Variant" information available for 3CY5)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLOBIN	PS01033	Globin family profile.	HBB_BUBBU	2-145	2	B:3-146 D:3-146
1	GLOBIN	PS01033	Globin family profile.	HBA2_BUBBU	3-142	2	A:2-141 C:2-141

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLOBIN	PS01033	Globin family profile.	HBB_BUBBU	2-145	2	B:3-146 D:3-146
1	GLOBIN	PS01033	Globin family profile.	HBA2_BUBBU	3-142	2	A:2-141 C:2-141

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLOBIN	PS01033	Globin family profile.	HBB_BUBBU	2-145	1	B:3-146 -
1	GLOBIN	PS01033	Globin family profile.	HBA2_BUBBU	3-142	1	A:2-141 -

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLOBIN	PS01033	Globin family profile.	HBB_BUBBU	2-145	1	- D:3-146
1	GLOBIN	PS01033	Globin family profile.	HBA2_BUBBU	3-142	1	- C:2-141

(no "Exon" information available for 3CY5)

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:141
 aligned with HBA2_BUBBU | Q9TSN8 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:141
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141 
           HBA2_BUBBU     2 VLSAADKSNIQAAWGKVGGHAADYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGAKVANALTKAVGHLDDLPGALSELSDLHAHKLRVDPVNFKLLSHSLLVTLASHLPNDFTPAVHASLDKFLASVSTVLTSKYR 142
               SCOP domains d3cy5a_ A: automated matches                                                                                                                  SCOP domains
               CATH domains 3cy5A00 A:1-141 Globins                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -GLOBIN  PDB: A:2-141 UniProt: 3-142                                                                                                          PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cy5 A   1 VLSAADKSNIQAAWGKVGGHAADYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGAKVANALTKAVGHLDDLPGALSELSDLHAHKLRVDPVNFKLLSHSLLVTLASHLPNDFTPAVHASLDKFLASVSTVLTSKYR 141
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain B from PDB  Type:PROTEIN  Length:145
 aligned with HBB_BUBBU | P67820 from UniProtKB/Swiss-Prot  Length:145

    Alignment length:145
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140     
            HBB_BUBBU     1 MLTAEEKAAVTAFWGKVHVDEVGGEALGRLLVVYPWTQRFFESFGDLSTADAVMNNPKVKAHGKKVLDSFSNGMKHLDDLKGTFAALSELHCDKLHVDPENFKLLGNVLVVVLARHFGKEFTPVLQADFQKVVAGVANALAHRYH 145
               SCOP domains d3cy5b_ B: automated matches                                                                                                                      SCOP domains
               CATH domains 3cy5B00 B:2-146 Globins                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -GLOBIN  PDB: B:3-146 UniProt: 2-145                                                                                                              PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cy5 B   2 MLTAEEKAAVTAFWGKVHVDEVGGEALGRLLVVYPWTQRFFESFGDLSTADAVMNNPKVKAHGKKVLDSFSNGMKHLDDLKGTFAALSELHCDKLHVDPENFKLLGNVLVVVLARHFGKEFTPVLQADFQKVVAGVANALAHRYH 146
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141

Chain C from PDB  Type:PROTEIN  Length:141
 aligned with HBA2_BUBBU | Q9TSN8 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:141
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141 
           HBA2_BUBBU     2 VLSAADKSNIQAAWGKVGGHAADYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGAKVANALTKAVGHLDDLPGALSELSDLHAHKLRVDPVNFKLLSHSLLVTLASHLPNDFTPAVHASLDKFLASVSTVLTSKYR 142
               SCOP domains d3cy5c_ C: automated matches                                                                                                                  SCOP domains
               CATH domains 3cy5C00 C:1-141 Globins                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -GLOBIN  PDB: C:2-141 UniProt: 3-142                                                                                                          PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cy5 C   1 VLSAADKSNIQAAWGKVGGHAADYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGAKVANALTKAVGHLDDLPGALSELSDLHAHKLRVDPVNFKLLSHSLLVTLASHLPNDFTPAVHASLDKFLASVSTVLTSKYR 141
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain D from PDB  Type:PROTEIN  Length:145
 aligned with HBB_BUBBU | P67820 from UniProtKB/Swiss-Prot  Length:145

    Alignment length:145
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140     
            HBB_BUBBU     1 MLTAEEKAAVTAFWGKVHVDEVGGEALGRLLVVYPWTQRFFESFGDLSTADAVMNNPKVKAHGKKVLDSFSNGMKHLDDLKGTFAALSELHCDKLHVDPENFKLLGNVLVVVLARHFGKEFTPVLQADFQKVVAGVANALAHRYH 145
               SCOP domains d3cy5d_ D: automated matches                                                                                                                      SCOP domains
               CATH domains 3cy5D00 D:2-146 Globins                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -GLOBIN  PDB: D:3-146 UniProt: 2-145                                                                                                              PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cy5 D   2 MLTAEEKAAVTAFWGKVHVDEVGGEALGRLLVVYPWTQRFFESFGDLSTADAVMNNPKVKAHGKKVLDSFSNGMKHLDDLKGTFAALSELHCDKLHVDPENFKLLGNVLVVVLARHFGKEFTPVLQADFQKVVAGVANALAHRYH 146
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141

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 Unit

Classes(

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Folds(

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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)

Buffalo (Bubalus bubalis) [TaxId: 89462] (1)

1a	d3cy5a_	A:
1b	d3cy5b_	B:
1c	d3cy5c_	C:
1d	d3cy5d_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Globin-like (786)

Homologous Superfamily: Globins (743)

Domestic water buffalo (Bubalus bubalis) (1)

1a	3cy5B00	B:2-146
1b	3cy5D00	D:2-146
1c	3cy5A00	A:1-141
1d	3cy5C00	C:1-141

(no "Pfam Domain" information available for 3CY5)

Asymmetric Unit(hide GO term definitions)

Chain A,C (HBA2_BUBBU | Q9TSN8)

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_BUBBU | P67820)

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.

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2qu0	CRYSTAL STRUCTURE DETERMINATION OF SHEEP METHEMOGLOBIN AT 2.7 ANGSTROM RESOLUTION
2ri4	CRYSTAL STRUCTURE DETERMINATION OF GOAT METHEMOGLOBIN AT 2.7 ANGSTROM

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