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Asym./Biol. Unit (Jmol Viewer)

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Title :   STRUCTURE OF HBII-III-CN FROM LUCINA PECTINATA AT PH 5.0

Authors :   J. A. Gavira, C. R. Ruiz-Martinez, C. A. Nieves-Marrero, R. A. Estremer Andujar, J. Lopez-Garriga, J. M. Garcia-Ruiz

Date :   02 Dec 10 (Deposition) - 07 Dec 11 (Release) - 07 Dec 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.76

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

Keywords :   Oxygen Carrier, Oxygen Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. R. Ruiz-Martinez, C. A. Nieves-Marrero, R. A. Estremera-Andujar, J. Lopez-Garriga, J. M. Garcia-Ruiz, J. A. Gavira
New Crystallographic Structure Of Hbii-Iii-Oxy And Cn Forms From Lucina Pectinata.
To Be Published
PubMed: search

Molecule 1 - HEMOGLOBIN II
	Chains	:	A
	Organism Common	:	CLAM
	Organism Scientific	:	LUCINA PECTINATA
	Organism Taxid	:	29163
	Strain	:	HBII
	Tissue	:	CTENIDIA

Molecule 2 - HEMOGLOBIN III
	Chains	:	B
	Organism Common	:	CLAM
	Organism Scientific	:	LUCINA PECTINATA
	Organism Taxid	:	29163
	Strain	:	HBIII
	Tissue	:	CTENIDIA

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (5, 10)

No.	Name	Count	Type	Full Name
1	ACE	1	Mod. Amino Acid	ACETYL GROUP
2	CYN	2	Ligand/Ion	CYANIDE ION
3	FMT	3	Ligand/Ion	FORMIC ACID
4	GOL	2	Ligand/Ion	GLYCEROL
5	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:40 , PRO A:43 , PHE A:44 , LEU A:47 , GLN A:65 , VAL A:68 , PHE A:69 , MET A:73 , LEU A:96 , HIS A:97 , ARG A:100 , ILE A:102 , ASP A:106 , LEU A:107 , TYR A:111 , HOH A:157 , HOH A:173 , HOH A:179 , HOH A:188 , CYN A:501 , LYS B:93 , HOH B:187 , HOH B:198	BINDING SITE FOR RESIDUE HEM A 500
2	AC2	SOFTWARE	TYR A:30 , GLN A:65 , PHE A:69 , HEM A:500	BINDING SITE FOR RESIDUE CYN A 501
3	AC3	SOFTWARE	THR A:4 , GLN A:7 , GLY A:49 , LEU A:51 , HOH A:213 , HOH A:277	BINDING SITE FOR RESIDUE GOL A 152
4	AC4	SOFTWARE	THR A:4 , ASN A:5 , PRO A:6 , LYS B:13 , SER B:17 , ASP B:79	BINDING SITE FOR RESIDUE FMT A 153
5	AC5	SOFTWARE	GLN A:55 , ASN A:59 , GLU A:133 , VAL A:134	BINDING SITE FOR RESIDUE FMT A 154
6	AC6	SOFTWARE	LYS A:92 , THR B:41 , PRO B:44 , PHE B:45 , GLN B:66 , VAL B:69 , PHE B:70 , MET B:74 , MET B:94 , LEU B:97 , HIS B:98 , ARG B:101 , ILE B:103 , GLU B:107 , LEU B:108 , TYR B:112 , HOH B:163 , HOH B:164 , HOH B:170 , HOH B:192 , HOH B:207 , HOH B:211 , CYN B:501	BINDING SITE FOR RESIDUE HEM B 500
7	AC7	SOFTWARE	TYR B:31 , GLN B:66 , HEM B:500	BINDING SITE FOR RESIDUE CYN B 501
8	AC8	SOFTWARE	HOH A:188 , HOH A:211 , GLN B:92 , HOH B:187	BINDING SITE FOR RESIDUE GOL B 153
9	AC9	SOFTWARE	ASP B:40 , GLU B:107	BINDING SITE FOR RESIDUE FMT B 154

(no "SS Bond" information available for 3PT8)

(no "Cis Peptide Bond" information available for 3PT8)

(no "SAP(SNP)/Variant" information available for 3PT8)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLOBIN	PS01033	Globin family profile.	GLB3_PHAPT	3-103	1	B:2-102
1	GLOBIN	PS01033	Globin family profile.	GLB2_PHAPT	4-143	1	A:3-143

(no "Exon" information available for 3PT8)

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:152
 aligned with GLB2_PHAPT | P41261 from UniProtKB/Swiss-Prot  Length:151

    Alignment length:152
                                                                                                                85                                                                  
                                                                                                              84 |                                                                  
                                    10        20        30        40        50        60        70        80   | |  89        99       109       119       129       139       149  
           GLB2_PHAPT     1 MTTLTNPQKAAIRSSWSKFMDNGVSNGQGFYMDLFKAHPETLTPFKSLFGGLTLAQLQDNPKMKAQSLVFCNGMSSFVDHLDDN-MLVVLIQKMAKLHNNRGIRASDLRTAYDILIHYMEDHNHMVGGAKDAWEVFVGFICKTLGDYMKELS 151
               SCOP domains d3pt8a_ A: automated matches                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---GLOBIN  PDB: A:3-143 UniProt: 4-143                                                                                                          -------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pt8 A   0 xTTLTNPQKAAIRSSWSKFMDNGVSNGQGFYMDLFKAHPETLTPFKSLFGGLTLAQLQDNPKMKAQSLVFCNGMSSFVDHLDDNDMLVVLIQKMAKLHNNRGIRASDLRTAYDILIHYMEDHNHMVGGAKDAWEVFVGFICKTLGDYMKELS 151
                            |        9        19        29        39        49        59        69        79        89        99       109       119       129       139       149  
                            0-ACE

Chain A from PDB  Type:PROTEIN  Length:152
 aligned with Q86G74_PHAPT | Q86G74 from UniProtKB/TrEMBL  Length:152

    Alignment length:152
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150  
         Q86G74_PHAPT     1 MTTLTNPQKAAIRSSWSKFMDNGVSNGQGFYMDLFKAHPETLTPFKSLFGGLTLAQLQDNPKMKAQSLVFCNGMSSFVDHLDDNDMLVVLIQKMAKLHNNRGIRASDLRTAYDILIHYMEDHNHMVGGAKDAWEVFVGFICKTLGDYMKELS 152
               SCOP domains d3pt8a_ A: automated matches                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pt8 A   0 xTTLTNPQKAAIRSSWSKFMDNGVSNGQGFYMDLFKAHPETLTPFKSLFGGLTLAQLQDNPKMKAQSLVFCNGMSSFVDHLDDNDMLVVLIQKMAKLHNNRGIRASDLRTAYDILIHYMEDHNHMVGGAKDAWEVFVGFICKTLGDYMKELS 151
                            |        9        19        29        39        49        59        69        79        89        99       109       119       129       139       149  
                            0-ACE

Chain B from PDB  Type:PROTEIN  Length:152
 aligned with A7UAU9_PHAPT | A7UAU9 from UniProtKB/TrEMBL  Length:153

    Alignment length:152
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151  
         A7UAU9_PHAPT     2 SSGLTGPQKAALKSSWSRFMDNAVTNGTNFYMDLFKAYPDTLTPFKSLFEDVSFNQMTDHPTMKAQALVFCNGMSSFVDNLDDHEVLVVLLQKMAKLHFNRGIRIKELRDGYGVLLRYLEDHCHVEGSTKNAWEDFIAYICRVQGDFMKERL 153
               SCOP domains d3pt8b_ B: automated matches                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pt8 B   1 SSGLTGPQKAALKSSWSRFMNNAVTNGTNFYMDLFKAYPDTLTPFKSLFQNVSFNQMTNHPTMKAQSLVFCNGMSSFVDNLDDHEVLVVLLQKMAKLHFNRGIRIKELRDGYGTLLRYLEDHCHVEGSTKNAWEDFIAYICRVQGDFMKERL 152
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain B from PDB  Type:PROTEIN  Length:152
 aligned with GLB3_PHAPT | P41262 from UniProtKB/Swiss-Prot  Length:153

    Alignment length:152
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151  
           GLB3_PHAPT     2 SSGLTGPQKAALKSSWSRFMDNAVTNGTNFYMDLFKAYPDTLTPFKSLFEDVSFNQMTDHPTMKAQALVFCDGMSSFVDNLDDHEVLVVLLQKMAKLHFNRGIRIKELRDGYGVLLRYLEDHCHVEGSTKNAWEDFIAYICRVQGDFMKERL 153
               SCOP domains d3pt8b_ B: automated matches                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -GLOBIN  PDB: B:2-102 UniProt: 3-103                                                                  -------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pt8 B   1 SSGLTGPQKAALKSSWSRFMNNAVTNGTNFYMDLFKAYPDTLTPFKSLFQNVSFNQMTNHPTMKAQSLVFCNGMSSFVDNLDDHEVLVVLLQKMAKLHFNRGIRIKELRDGYGTLLRYLEDHCHVEGSTKNAWEDFIAYICRVQGDFMKERL 152
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

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: automated matches (42)

Protein domain: automated matches (42)

Clam (Lucina pectinata) [TaxId: 244486] (7)

1a	d3pt8a_	A:
1b	d3pt8b_	B:

(no "CATH Domain" information available for 3PT8)

(no "Pfam Domain" information available for 3PT8)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (Q86G74_PHAPT | Q86G74)

molecular function
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	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.

Chain A (GLB2_PHAPT | P41261)

molecular function
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain B (A7UAU9_PHAPT | A7UAU9)

molecular function
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	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.

Chain B (GLB3_PHAPT | P41262)

molecular function
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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UniProtKB/Swiss-Prot
	A7UAU9_PHAPT \| A7UAU9	:	3pt7
	GLB2_PHAPT \| P41261	:	2olp 3pi1 3pi2 3pi3 3pi4 3pt7
	GLB3_PHAPT \| P41262	:	3pt7
	Q86G74_PHAPT \| Q86G74	:	2olp 3pi1 3pi2 3pi3 3pi4 3pt7

2opl	LUCINA PECTINATA HBII-OXY PH7
3pi1	LUCINA PECTINATA HBII-OXY PH9
3pi2	LUCINA PECTINATA HBII-OXY PH8
3pi3	LUCINA PECTINATA HBII-OXY PH5
3pi4	LUCINA PECTINATA HBII-OXY PH4
3pt7

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 10)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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Gene Ontology (7, 24)

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