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Asym./Biol. Unit (Jmol Viewer)

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

Title :   THE X-RAY STRUCTURE DETERMINATION OF BOVINE CARBONMONOXY HB AT 2.1 A RESOLUTION AND ITS RELATIONSHIP TO THE QUATERNARY STRUCTURE OF OTHER HB CRYSTAL FORMS

Authors :   M. K. Safo, D. J. Abraham

Date :   11 Sep 00 (Deposition) - 06 Jun 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Hemoglobin Tetramer, R-State, Quaternary Structure, Oxygen Storage/Transport Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. K. Safo, D. J. Abraham
The X-Ray Structure Determination Of Bovine Carbonmonoxy Hemoglobin At 2. 1 A Resoultion And Its Relationship To The Quaternary Structures Of Other Hemoglobin Crystal Froms.
Protein Sci. V. 10 1091 2001
PubMed-ID: 11369847 | Reference-DOI: 10.1110/PS.48301
(for further references see the PDB file header)

Molecule 1 - HEMOGLOBIN ALPHA CHAIN
	Chains	:	A, C
	Organism Common	:	CATTLE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913
	Tissue	:	BLOOD

Molecule 2 - HEMOGLOBIN BETA CHAIN
	Chains	:	B, D
	Organism Common	:	CATTLE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913
	Tissue	:	BLOOD

		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	CMO	4	Ligand/Ion	CARBON MONOXIDE
2	HEM	4	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:58 , VAL A:62 , HEM A:143	BINDING SITE FOR RESIDUE CMO A 142
2	AC2	SOFTWARE	TYR A:42 , HIS A:45 , HIS A:58 , LYS A:61 , LEU A:66 , HIS A:87 , LEU A:91 , VAL A:93 , ASN A:97 , PHE A:98 , LEU A:101 , VAL A:132 , LEU A:136 , CMO A:142 , HOH A:830 , HOH A:854	BINDING SITE FOR RESIDUE HEM A 143
3	AC3	SOFTWARE	HIS B:263 , VAL B:267 , HEM B:348	BINDING SITE FOR RESIDUE CMO B 347
4	AC4	SOFTWARE	THR B:238 , PHE B:241 , PHE B:242 , HIS B:263 , LYS B:266 , SER B:270 , LEU B:291 , HIS B:292 , LEU B:296 , VAL B:298 , ASN B:302 , PHE B:303 , CMO B:347 , HOH B:930 , LYS D:608	BINDING SITE FOR RESIDUE HEM B 348
5	AC5	SOFTWARE	HIS C:458 , VAL C:462 , HEM C:543	BINDING SITE FOR RESIDUE CMO C 542
6	AC6	SOFTWARE	TYR C:442 , PHE C:443 , HIS C:445 , HIS C:458 , LYS C:461 , GLU C:482 , HIS C:487 , LEU C:491 , VAL C:493 , ASN C:497 , PHE C:498 , LEU C:501 , LEU C:536 , CMO C:542 , HOH C:877	BINDING SITE FOR RESIDUE HEM C 543
7	AC7	SOFTWARE	HIS D:663 , VAL D:667 , HEM D:748	BINDING SITE FOR RESIDUE CMO D 747
8	AC8	SOFTWARE	ALA C:404 , PHE D:641 , PHE D:642 , HIS D:663 , LYS D:666 , VAL D:667 , SER D:670 , LEU D:688 , HIS D:692 , LEU D:696 , VAL D:698 , ASN D:702 , PHE D:703 , LEU D:706 , LEU D:741 , CMO D:747	BINDING SITE FOR RESIDUE HEM D 748

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

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

Asymmetric/Biological Unit (8, 16)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_HBA_BOVIN_001 *	H	90	Y	HBA_BOVIN	---	---	A C	H	89 489	Y
2	UniProt	VAR_HBA_BOVIN_002 *	N	132	S	HBA_BOVIN	---	---	A C	N	131 531	S
3	UniProt	VAR_HBB_BOVIN_001 *	G	15	S	HBB_BOVIN	---	---	B D	G	216 616	S
4	UniProt	VAR_HBB_BOVIN_002 *	K	18	H	HBB_BOVIN	---	---	B D	K	219 619	H
5	UniProt	VAR_HBB_BOVIN_003 *	D	20	G	HBB_BOVIN	---	---	B D	D	221 621	G
6	UniProt	VAR_HBB_BOVIN_004 *	S	43	T	HBB_BOVIN	---	---	B D	S	244 644	T
7	UniProt	VAR_HBB_BOVIN_005 *	K	119	N	HBB_BOVIN	---	---	B D	K	320 720	N
8	UniProt	VAR_HBB_BOVIN_006 *	K	131	Q	HBB_BOVIN	---	---	B D	K	332 732	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.	HBB_BOVIN	2-145	2	B:203-346 D:603-746
1	GLOBIN	PS01033	Globin family profile.	HBA_BOVIN	3-142	2	A:2-141 C:402-541

Asymmetric/Biological Unit (6, 12)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSBTAT00000037545	1	ENSBTAE00000380516	chr25:669652-669785	134	HBA_BOVIN	1-32	32	2	A:1-31 C:401-431	31 31
1.2	ENSBTAT00000037545	2	ENSBTAE00000412716	chr25:669887-670091	205	HBA_BOVIN	32-100	69	2	A:31-99 C:431-499	69 69
1.3	ENSBTAT00000037545	3	ENSBTAE00000409296	chr25:670196-670419	224	HBA_BOVIN	101-142	42	2	A:100-141 C:500-541	42 42

2.1	ENSBTAT00000045694	1	ENSBTAE00000377266	chr15:47825662-47825799	138	HBB_BOVIN	1-29	29	2	B:202-230 D:602-630	29 29
2.2	ENSBTAT00000045694	2	ENSBTAE00000383380	chr15:47825928-47826150	223	HBB_BOVIN	29-103	75	2	B:230-304 D:630-704	75 75
2.3	ENSBTAT00000045694	3	ENSBTAE00000339283	chr15:47827051-47827179	129	HBB_BOVIN	104-145	42	2	B:305-346 D:705-746	42 42

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_BOVIN | P01966 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:141
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141 
            HBA_BOVIN     2 VLSAADKGNVKAAWGKVGGHAAEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGAKVAAALTKAVEHLDDLPGALSELSDLHAHKLRVDPVNFKLLSHSLLVTLASHLPSDFTPAVHASLDKFLANVSTVLTSKYR 142
               SCOP domains d1fsxa_ A: Hemoglobin, alpha-chain                                                                                                            SCOP domains
               CATH domains 1fsxA00 A:1-141 Globins                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -GLOBIN  PDB: A:2-141 UniProt: 3-142                                                                                                          PROSITE (2)
           Transcript 1 (1) Exon 1.1  PDB: A:1-31          --------------------------------------------------------------------Exon 1.3  PDB: A:100-141 UniProt: 101-142  Transcript 1 (1)
           Transcript 1 (2) ------------------------------Exon 1.2  PDB: A:31-99 UniProt: 32-100                               ------------------------------------------ Transcript 1 (2)
                 1fsx A   1 VLSAADKGNVKAAWGKVGGHAAEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGAKVAAALTKAVEHLDDLPGALSELSDLHAHKLRVDPVNFKLLSHSLLVTLASHLPSDFTPAVHASLDKFLANVSTVLTSKYR 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_BOVIN | P02070 from UniProtKB/Swiss-Prot  Length:145

    Alignment length:145
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140     
            HBB_BOVIN     1 MLTAEEKAAVTAFWGKVKVDEVGGEALGRLLVVYPWTQRFFESFGDLSTADAVMNNPKVKAHGKKVLDSFSNGMKHLDDLKGTFAALSELHCDKLHVDPENFKLLGNVLVVVLARNFGKEFTPVLQADFQKVVAGVANALAHRYH 145
               SCOP domains d1fsxb_ B: Hemoglobin, beta-chain                                                                                                                 SCOP domains
               CATH domains 1fsxB00 B:202-346 Globins                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -GLOBIN  PDB: B:203-346 UniProt: 2-145                                                                                                            PROSITE
           Transcript 2 (1) Exon 2.1  PDB: B:202-230     --------------------------------------------------------------------------Exon 2.3  PDB: B:305-346 UniProt: 104-145  Transcript 2 (1)
           Transcript 2 (2) ----------------------------Exon 2.2  PDB: B:230-304 UniProt: 29-103                                   ------------------------------------------ Transcript 2 (2)
                 1fsx B 202 MLTAEEKAAVTAFWGKVKVDEVGGEALGRLLVVYPWTQRFFESFGDLSTADAVMNNPKVKAHGKKVLDSFSNGMKHLDDLKGTFAALSELHCDKLHVDPENFKLLGNVLVVVLARNFGKEFTPVLQADFQKVVAGVANALAHRYH 346
                                   211       221       231       241       251       261       271       281       291       301       311       321       331       341

Chain C from PDB  Type:PROTEIN  Length:141
 aligned with HBA_BOVIN | P01966 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:141
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141 
            HBA_BOVIN     2 VLSAADKGNVKAAWGKVGGHAAEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGAKVAAALTKAVEHLDDLPGALSELSDLHAHKLRVDPVNFKLLSHSLLVTLASHLPSDFTPAVHASLDKFLANVSTVLTSKYR 142
               SCOP domains d1fsxc_ C: Hemoglobin, alpha-chain                                                                                                            SCOP domains
               CATH domains 1fsxC00 C:401-541 Globins                                                                                                                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------Y-----------------------------------------S---------- SAPs(SNPs)
                PROSITE (2) -GLOBIN  PDB: C:402-541 UniProt: 3-142                                                                                                        PROSITE (2)
           Transcript 1 (1) Exon 1.1  PDB: C:401-431       --------------------------------------------------------------------Exon 1.3  PDB: C:500-541 UniProt: 101-142  Transcript 1 (1)
           Transcript 1 (2) ------------------------------Exon 1.2  PDB: C:431-499 UniProt: 32-100                             ------------------------------------------ Transcript 1 (2)
                 1fsx C 401 VLSAADKGNVKAAWGKVGGHAAEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGAKVAAALTKAVEHLDDLPGALSELSDLHAHKLRVDPVNFKLLSHSLLVTLASHLPSDFTPAVHASLDKFLANVSTVLTSKYR 541
                                   410       420       430       440       450       460       470       480       490       500       510       520       530       540

Chain D from PDB  Type:PROTEIN  Length:145
 aligned with HBB_BOVIN | P02070 from UniProtKB/Swiss-Prot  Length:145

    Alignment length:145
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140     
            HBB_BOVIN     1 MLTAEEKAAVTAFWGKVKVDEVGGEALGRLLVVYPWTQRFFESFGDLSTADAVMNNPKVKAHGKKVLDSFSNGMKHLDDLKGTFAALSELHCDKLHVDPENFKLLGNVLVVVLARNFGKEFTPVLQADFQKVVAGVANALAHRYH 145
               SCOP domains d1fsxd_ D: Hemoglobin, beta-chain                                                                                                                 SCOP domains
               CATH domains 1fsxD00 D:602-746 Globins                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------S--H-G----------------------T---------------------------------------------------------------------------N-----------Q-------------- SAPs(SNPs)
                    PROSITE -GLOBIN  PDB: D:603-746 UniProt: 2-145                                                                                                            PROSITE
           Transcript 2 (1) Exon 2.1  PDB: D:602-630     --------------------------------------------------------------------------Exon 2.3  PDB: D:705-746 UniProt: 104-145  Transcript 2 (1)
           Transcript 2 (2) ----------------------------Exon 2.2  PDB: D:630-704 UniProt: 29-103                                   ------------------------------------------ Transcript 2 (2)
                 1fsx D 602 MLTAEEKAAVTAFWGKVKVDEVGGEALGRLLVVYPWTQRFFESFGDLSTADAVMNNPKVKAHGKKVLDSFSNGMKHLDDLKGTFAALSELHCDKLHVDPENFKLLGNVLVVVLARNFGKEFTPVLQADFQKVVAGVANALAHRYH 746
                                   611       621       631       641       651       661       671       681       691       701       711       721       731       741

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)

Cow (Bos taurus) [TaxId: 9913] (11)

1a	d1fsxa_	A:
1b	d1fsxc_	C:

Protein domain: Hemoglobin, beta-chain (292)

Cow (Bos taurus) [TaxId: 9913] (11)

2a	d1fsxb_	B:
2b	d1fsxd_	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)

Cattle (Bos taurus) (6)

1a	1fsxB00	B:202-346
1b	1fsxA00	A:1-141
1c	1fsxC00	C:401-541
1d	1fsxD00	D:602-746

(no "Pfam Domain" information available for 1FSX)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,C (HBA_BOVIN | P01966)

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: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_BOVIN | P02070)

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 1fsx)

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	1fsx
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(no "Related Entries Specified in the PDB File" available for 1FSX)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (8, 16)

PROSITE Motifs (1, 4)

Exons (6, 12)

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SCOP Domains (2, 4)

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