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Asym./Biol. Unit (Jmol Viewer)

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

Title :   SITE-SELECTIVE GLYCOSYLATION OF CYSTEINE-93 BETA ON THE SURFACE OF BOVINE HEMOGLOBIN AND ITS APPLICATION AS A NOVEL OXYGEN THERAPEUTIC

Authors :   V. S. Bhatt, Y. Zhang, G. Sun, P. G. Wang, A. F. Palmer

Date :   11 Mar 08 (Deposition) - 15 Apr 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.50

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

Keywords :   Hemoglobin, Glycosylation, Site-Selective, Oxygen Carrier, Blood Substitute, Heme, Iron, Oxygen Transport, Polymorphism, Transport, Oxygen Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. S. Bhatt, Y. Zhang, G. Sun, P. G. Wang, A. F. Palmer
Site-Selective Glycosylation Of Cysteine-93 Beta On The Surface Of Bovine Hemoglobin And Its Application As A Novel Oxygen Therapeutic
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - HEMOGLOBIN SUBUNIT ALPHA
	Chains	:	A, C
	Engineered	:	YES
	Gene	:	HBA
	Organism Common	:	CATTLE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913
	Synonym	:	HEMOGLOBIN ALPHA CHAIN, ALPHA-GLOBIN

Molecule 2 - HEMOGLOBIN SUBUNIT BETA
	Chains	:	B, D
	Engineered	:	YES
	Gene	:	HBB
	Organism Common	:	CATTLE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913
	Synonym	:	HEMOGLOBIN BETA CHAIN, BETA-GLOBIN

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 9)

No.	Name	Count	Type	Full Name
1	5DP	1	Ligand/Ion	5-(2,5-DIOXOPYRROLIDIN-1-YL)-N-[2-(2-{2-[(4-O-ALPHA-D-IDOPYRANOSYL-ALPHA-D-MANNOPYRANOSYL)OXY]ETHOXY}ETHOXY)ETHYL]PENTANAMIDE
2	HEM	4	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	O	4	Ligand/Ion	OXYGEN ATOM

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:83 , HIS A:87 , LEU A:91 , ASN A:97 , PHE A:98 , LEU A:101 , LEU A:136 , HOH A:144	BINDING SITE FOR RESIDUE HEM A 142
2	AC2	SOFTWARE	HIS A:58 , HOH A:144	BINDING SITE FOR RESIDUE O A 143
3	AC3	SOFTWARE	THR B:38 , PHE B:41 , PHE B:42 , PHE B:45 , HIS B:63 , HIS B:92 , LEU B:96 , ASN B:102 , PHE B:103 , LEU B:106 , LEU B:141	BINDING SITE FOR RESIDUE HEM B 147
4	AC4	SOFTWARE	PHE B:42 , HIS B:63	BINDING SITE FOR RESIDUE O B 148
5	AC5	SOFTWARE	ALA A:12 , LYS A:16 , TYR C:42 , HIS C:45 , HIS C:58 , LYS C:61 , LEU C:83 , LEU C:86 , HIS C:87 , LEU C:91 , ASN C:97 , PHE C:98 , LEU C:101 , LEU C:136	BINDING SITE FOR RESIDUE HEM C 142
6	AC6	SOFTWARE	PHE D:41 , PHE D:42 , HIS D:63 , LYS D:66 , SER D:70 , HIS D:92 , LEU D:96 , ASN D:102 , PHE D:103 , LEU D:106 , LEU D:141	BINDING SITE FOR RESIDUE HEM D 147
7	AC7	SOFTWARE	HIS D:63	BINDING SITE FOR RESIDUE O D 148
8	AC8	SOFTWARE	CYS B:93 , ASP B:94	BINDING SITE FOR RESIDUE 5DP B 1

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

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

Asymmetric/Biological Unit (8, 16)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_HBB_BOVIN_001 *	G	15	S	HBB_BOVIN	---	---	B/D	G	16	S
2	UniProt	VAR_HBB_BOVIN_002 *	K	18	H	HBB_BOVIN	---	---	B/D	K	19	H
3	UniProt	VAR_HBB_BOVIN_003 *	D	20	G	HBB_BOVIN	---	---	B/D	D	21	G
4	UniProt	VAR_HBB_BOVIN_004 *	S	43	T	HBB_BOVIN	---	---	B/D	S	44	T
5	UniProt	VAR_HBA_BOVIN_001 *	H	90	Y	HBA_BOVIN	---	---	A/C	H	89	Y
6	UniProt	VAR_HBB_BOVIN_005 *	K	119	N	HBB_BOVIN	---	---	B/D	K	120	N
7	UniProt	VAR_HBA_BOVIN_002 *	N	132	S	HBA_BOVIN	---	---	A/C	N	131	S
8	UniProt	VAR_HBB_BOVIN_006 *	K	131	Q	HBB_BOVIN	---	---	B/D	K	132	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:3-146 D:3-146
1	GLOBIN	PS01033	Globin family profile.	HBA_BOVIN	3-142	2	A:2-141 C:2-141

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:2-31 C:1-31	30 31
1.2	ENSBTAT00000037545	2	ENSBTAE00000412716	chr25:669887-670091	205	HBA_BOVIN	32-100	69	2	A:31-99 C:31-99	69 69
1.3	ENSBTAT00000037545	3	ENSBTAE00000409296	chr25:670196-670419	224	HBA_BOVIN	101-142	42	2	A:100-141 C:100-141	42 42

2.1	ENSBTAT00000045694	1	ENSBTAE00000377266	chr15:47825662-47825799	138	HBB_BOVIN	1-29	29	2	B:2-30 D:2-30	29 29
2.2	ENSBTAT00000045694	2	ENSBTAE00000383380	chr15:47825928-47826150	223	HBB_BOVIN	29-103	75	2	B:30-104 D:30-104	75 75
2.3	ENSBTAT00000045694	3	ENSBTAE00000339283	chr15:47827051-47827179	129	HBB_BOVIN	104-145	42	2	B:105-146 D:105-146	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:140
 aligned with HBA_BOVIN | P01966 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:140
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142
            HBA_BOVIN     3 LSAADKGNVKAAWGKVGGHAAEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGAKVAAALTKAVEHLDDLPGALSELSDLHAHKLRVDPVNFKLLSHSLLVTLASHLPSDFTPAVHASLDKFLANVSTVLTSKYR 142
               SCOP domains d3ciua1 A:2-141 Hemoglobin, alpha-chain                                                                                                      SCOP domains
               CATH domains 3ciuA00 A:2-141 Globins                                                                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------Y-----------------------------------------S---------- SAPs(SNPs)
                PROSITE (2) GLOBIN  PDB: A:2-141 UniProt: 3-142                                                                                                          PROSITE (2)
           Transcript 1 (1) Exon 1.1  PDB: A:2-31         --------------------------------------------------------------------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)
                 3ciu A   2 LSAADKGNVKAAWGKVGGHAAEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGAKVAAALTKAVEHLDDLPGALSELSDLHAHKLRVDPVNFKLLSHSLLVTLASHLPSDFTPAVHASLDKFLANVSTVLTSKYR 141
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141

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 d3ciub1 B:2-146 Hemoglobin, beta-chain                                                                                                            SCOP domains
               CATH domains 3ciuB00 B:2-146 Globins                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------S--H-G----------------------T---------------------------------------------------------------------------N-----------Q-------------- SAPs(SNPs)
                    PROSITE -GLOBIN  PDB: B:3-146 UniProt: 2-145                                                                                                              PROSITE
           Transcript 2 (1) Exon 2.1  PDB: B:2-30        --------------------------------------------------------------------------Exon 2.3  PDB: B:105-146 UniProt: 104-145  Transcript 2 (1)
           Transcript 2 (2) ----------------------------Exon 2.2  PDB: B:30-104 UniProt: 29-103                                    ------------------------------------------ Transcript 2 (2)
                 3ciu B   2 MLTAEEKAAVTAFWGKVKVDEVGGEALGRLLVVYPWTQRFFESFGDLSTADAVMNNPKVKAHGKKVLDSFSNGMKHLDDLKGTFAALSELHCDKLHVDPENFKLLGNVLVVVLARNFGKEFTPVLQADFQKVVAGVANALAHRYH 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 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 d3ciuc1 C:1-141 Hemoglobin, alpha-chain                                                                                                       SCOP domains
               CATH domains 3ciuC00 C:1-141 Globins                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------Y-----------------------------------------S---------- SAPs(SNPs)
                PROSITE (2) -GLOBIN  PDB: C:2-141 UniProt: 3-142                                                                                                          PROSITE (2)
           Transcript 1 (1) Exon 1.1  PDB: C:1-31          --------------------------------------------------------------------Exon 1.3  PDB: C:100-141 UniProt: 101-142  Transcript 1 (1)
           Transcript 1 (2) ------------------------------Exon 1.2  PDB: C:31-99 UniProt: 32-100                               ------------------------------------------ Transcript 1 (2)
                 3ciu C   1 VLSAADKGNVKAAWGKVGGHAAEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGAKVAAALTKAVEHLDDLPGALSELSDLHAHKLRVDPVNFKLLSHSLLVTLASHLPSDFTPAVHASLDKFLANVSTVLTSKYR 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_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 d3ciud1 D:2-146 Hemoglobin, beta-chain                                                                                                            SCOP domains
               CATH domains 3ciuD00 D:2-146 Globins                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------S--H-G----------------------T---------------------------------------------------------------------------N-----------Q-------------- SAPs(SNPs)
                    PROSITE -GLOBIN  PDB: D:3-146 UniProt: 2-145                                                                                                              PROSITE
           Transcript 2 (1) Exon 2.1  PDB: D:2-30        --------------------------------------------------------------------------Exon 2.3  PDB: D:105-146 UniProt: 104-145  Transcript 2 (1)
           Transcript 2 (2) ----------------------------Exon 2.2  PDB: D:30-104 UniProt: 29-103                                    ------------------------------------------ Transcript 2 (2)
                 3ciu D   2 MLTAEEKAAVTAFWGKVKVDEVGGEALGRLLVVYPWTQRFFESFGDLSTADAVMNNPKVKAHGKKVLDSFSNGMKHLDDLKGTFAALSELHCDKLHVDPENFKLLGNVLVVVLARNFGKEFTPVLQADFQKVVAGVANALAHRYH 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/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	d3ciua1	A:2-141
1b	d3ciuc1	C:1-141

Protein domain: Hemoglobin, beta-chain (292)

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

2a	d3ciub1	B:2-146
2b	d3ciud1	D:2-146

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	3ciuB00	B:2-146
1b	3ciuD00	D:2-146
1c	3ciuC00	C:1-141
1d	3ciuA00	A:2-141

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

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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(no "Related Entries Specified in the PDB File" available for 3CIU)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 9)

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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