3PI2 - JenaLib

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Title :   CRYSTALLOGRAPHIC STRUCTURE OF HBII-OXY FROM LUCINA PECTINATA AT PH 8.0

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

Date :   05 Nov 10 (Deposition) - 09 Nov 11 (Release) - 21 Dec 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A,B  (2x)
Biol. Unit 3: A,B  (4x)

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

Reference :   C. A. Nieves-Marrero, C. R. Ruiz-Martinez, R. A. Estremera-Andujar, J. Lopez-Garriga, J. M. Garcia-Ruiz, J. A. Gavira
Ph-Dependence Crystallographic Studies Of The Oxygen Carrie Hemoglobin Ii From Lucina Pectinata
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - HEMOGLOBIN II
	Chains	:	A, B
	Organism Common	:	LUCINA PECTINATA
	Organism Scientific	:	PHACOIDES PECTINATUS
	Organism Taxid	:	244486
	Synonym	:	LUCINA PECTINATA

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 7)

No.	Name	Count	Type	Full Name
1	ACE	2	Mod. Amino Acid	ACETYL GROUP
2	FMT	1	Ligand/Ion	FORMIC ACID
3	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
4	OXY	2	Ligand/Ion	OXYGEN MOLECULE

Biological Unit 1 (4, 7)

No.	Name	Count	Type	Full Name
1	ACE	2	Mod. Amino Acid	ACETYL GROUP
2	FMT	1	Ligand/Ion	FORMIC ACID
3	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
4	OXY	2	Ligand/Ion	OXYGEN MOLECULE

Biological Unit 2 (4, 14)

No.	Name	Count	Type	Full Name
1	ACE	4	Mod. Amino Acid	ACETYL GROUP
2	FMT	2	Ligand/Ion	FORMIC ACID
3	HEM	4	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
4	OXY	4	Ligand/Ion	OXYGEN MOLECULE

Biological Unit 3 (4, 28)

No.	Name	Count	Type	Full Name
1	ACE	8	Mod. Amino Acid	ACETYL GROUP
2	FMT	4	Ligand/Ion	FORMIC ACID
3	HEM	8	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
4	OXY	8	Ligand/Ion	OXYGEN MOLECULE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO A:43 , PHE A:44 , LEU A:47 , GLN A:65 , VAL A:68 , PHE A:69 , MET A:73 , MET A:93 , LEU A:96 , HIS A:97 , ARG A:100 , ILE A:102 , ASP A:106 , LEU A:107 , TYR A:111 , OXY A:501 , HOH A:607 , HOH A:615 , HOH A:617 , HOH A:652 , HOH A:681 , LYS B:92 , LEU B:96	BINDING SITE FOR RESIDUE HEM A 500
2	AC2	SOFTWARE	TYR A:30 , PHE A:44 , GLN A:65 , HEM A:500	BINDING SITE FOR RESIDUE OXY A 501
3	AC3	SOFTWARE	LYS A:92 , LEU A:96 , PRO B:43 , PHE B:44 , LEU B:47 , GLN B:65 , VAL B:68 , PHE B:69 , MET B:73 , MET B:93 , LEU B:96 , HIS B:97 , ARG B:100 , ILE B:102 , LEU B:107 , TYR B:111 , OXY B:202 , HOH B:307 , HOH B:314 , HOH B:326 , HOH B:332 , HOH B:379 , HOH B:426	BINDING SITE FOR RESIDUE HEM B 201
4	AC4	SOFTWARE	TYR B:30 , PHE B:44 , GLN B:65 , HEM B:201	BINDING SITE FOR RESIDUE OXY B 202
5	AC5	SOFTWARE	GLU B:39 , ASP B:106	BINDING SITE FOR RESIDUE FMT B 203

(no "SS Bond" information available for 3PI2)

(no "Cis Peptide Bond" information available for 3PI2)

(no "SAP(SNP)/Variant" information available for 3PI2)

Asymmetric Unit (1, 2)

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

Biological Unit 1 (1, 2)

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

Biological Unit 2 (1, 4)

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

Biological Unit 3 (1, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLOBIN	PS01033	Globin family profile.	GLB2_PHAPT	4-143	8	A:3-143 B:3-143

(no "Exon" information available for 3PI2)

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: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 d3pi2a_ A: automated matches                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---GLOBIN  PDB: A:3-143 UniProt: 4-143                                                                                                          -------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pi2 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 d3pi2a_ A: automated matches                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pi2 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 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 d3pi2b_ B: automated matches                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---GLOBIN  PDB: B:3-143 UniProt: 4-143                                                                                                          -------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pi2 B   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 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 d3pi2b_ B: automated matches                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pi2 B   0 xTTLTNPQKAAIRSSWSKFMDNGVSNGQGFYMDLFKAHPETLTPFKSLFGGLTLAQLQDNPKMKAQSLVFCNGMSSFVDHLDDNDMLVVLIQKMAKLHNNRGIRASDLRTAYDILIHYMEDHNHMVGGAKDAWEVFVGFICKTLGDYMKELS 151
                            |        9        19        29        39        49        59        69        79        89        99       109       119       129       139       149  
                            0-ACE

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(

)

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	d3pi2a_	A:
1b	d3pi2b_	B:

(no "CATH Domain" information available for 3PI2)

(no "Pfam Domain" information available for 3PI2)

Asymmetric Unit(hide GO term definitions)

Chain A,B (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,B (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.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3pi2)

Biological Units
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	Q86G74_PHAPT \| Q86G74
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UniProtKB/Swiss-Prot
	GLB2_PHAPT \| P41261	:	2olp 3pi1 3pi3 3pi4 3pt7 3pt8
	Q86G74_PHAPT \| Q86G74	:	2olp 3pi1 3pi3 3pi4 3pt7 3pt8

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 7)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Exons (0, 0)

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Gene Ontology (7, 12)

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