3PI1 - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTALLOGRAPHIC STRUCTURE OF HBII-OXY FROM LUCINA PECTINATA AT PH 9.0

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) - 09 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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	:	LUCINA PECTINATA
	Organism Taxid	:	244486

		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 (3, 5)

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

Biological Unit 1 (3, 5)

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

Biological Unit 2 (3, 10)

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

Biological Unit 3 (3, 20)

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

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO A:43 , PHE A:44 , GLN A:65 , VAL A:68 , MET A:93 , LEU A:96 , HIS A:97 , ARG A:100 , ILE A:102 , ASP A:106 , LEU A:107 , TYR A:111 , HOH A:234 , HOH A:235 , HOH A:239 , HOH A:241 , HOH A:245 , OXY A:501 , LYS B:92	BINDING SITE FOR RESIDUE HEM A 500
2	AC2	SOFTWARE	TYR A:30 , 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 , GLN B:65 , VAL B:68 , PHE B:69 , MET B:93 , LEU B:96 , HIS B:97 , ARG B:100 , ILE B:102 , LEU B:107 , TYR B:111 , HOH B:176 , HOH B:184 , HOH B:189 , HOH B:195 , HOH B:197 , OXY B:501	BINDING SITE FOR RESIDUE HEM B 500
4	AC4	SOFTWARE	TYR B:30 , GLN B:65 , HEM B:500	BINDING SITE FOR RESIDUE OXY B 501

(no "SS Bond" information available for 3PI1)

(no "Cis Peptide Bond" information available for 3PI1)

(no "SAP(SNP)/Variant" information available for 3PI1)

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 3PI1)

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 d3pi1a_ A: automated matches                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---GLOBIN  PDB: A:3-143 UniProt: 4-143                                                                                                          -------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pi1 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 d3pi1a_ A: automated matches                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pi1 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:151
 aligned with GLB2_PHAPT | P41261 from UniProtKB/Swiss-Prot  Length:151

    Alignment length:151
                                                                                                               85                                                                  
                                                                                                             84 |                                                                  
                                    11        21        31        41        51        61        71        81  | |   90       100       110       120       130       140       150 
           GLB2_PHAPT     2 TTLTNPQKAAIRSSWSKFMDNGVSNGQGFYMDLFKAHPETLTPFKSLFGGLTLAQLQDNPKMKAQSLVFCNGMSSFVDHLDDN-MLVVLIQKMAKLHNNRGIRASDLRTAYDILIHYMEDHNHMVGGAKDAWEVFVGFICKTLGDYMKELS 151
               SCOP domains d3pi1b_ B: automated matches                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --GLOBIN  PDB: B:3-143 UniProt: 4-143                                                                                                          -------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pi1 B   1 TTLTNPQKAAIRSSWSKFMDNGVSNGQGFYMDLFKAHPETLTPFKSLFGGLTLAQLQDNPKMKAQSLVFCNGMSSFVDHLDDNDMLVVLIQKMAKLHNNRGIRASDLRTAYDILIHYMEDHNHMVGGAKDAWEVFVGFICKTLGDYMKELS 151
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain B from PDB  Type:PROTEIN  Length:151
 aligned with Q86G74_PHAPT | Q86G74 from UniProtKB/TrEMBL  Length:152

    Alignment length:151
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151 
         Q86G74_PHAPT     2 TTLTNPQKAAIRSSWSKFMDNGVSNGQGFYMDLFKAHPETLTPFKSLFGGLTLAQLQDNPKMKAQSLVFCNGMSSFVDHLDDNDMLVVLIQKMAKLHNNRGIRASDLRTAYDILIHYMEDHNHMVGGAKDAWEVFVGFICKTLGDYMKELS 152
               SCOP domains d3pi1b_ B: automated matches                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pi1 B   1 TTLTNPQKAAIRSSWSKFMDNGVSNGQGFYMDLFKAHPETLTPFKSLFGGLTLAQLQDNPKMKAQSLVFCNGMSSFVDHLDDNDMLVVLIQKMAKLHNNRGIRASDLRTAYDILIHYMEDHNHMVGGAKDAWEVFVGFICKTLGDYMKELS 151
                                    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 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	d3pi1a_	A:
1b	d3pi1b_	B:

(no "CATH Domain" information available for 3PI1)

(no "Pfam Domain" information available for 3PI1)

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 3pi1)

Biological Units
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	Q86G74_PHAPT \| Q86G74
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UniProtKB/Swiss-Prot
	GLB2_PHAPT \| P41261	:	2olp 3pi2 3pi3 3pi4 3pt7 3pt8
	Q86G74_PHAPT \| Q86G74	:	2olp 3pi2 3pi3 3pi4 3pt7 3pt8

Description

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Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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