4HRT - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   SCAPHARCA TETRAMERIC HEMOGLOBIN, UNLIGANDED

Authors :   W. E. Royer

Date :   28 Oct 12 (Deposition) - 12 Dec 12 (Release) - 08 Jan 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.46

Chains :   Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D  (1x)
Biol. Unit 2: E,F,G,H  (1x)

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

Reference :   L. Ronda, S. Bettati, E. R. Henry, T. Kashav, J. M. Sanders, W. E. Royer, A. Mozzarelli
Tertiary And Quaternary Allostery In Tetrameric Hemoglobin From Scapharca Inaequivalvis.
Biochemistry V. 52 2108 2013
PubMed-ID: 23458680 | Reference-DOI: 10.1021/BI301620X

Molecule 1 - GLOBIN-2 A CHAIN
	Chains	:	A, C, E, G
	Organism Common	:	INEQUIVALVE ARK
	Organism Scientific	:	SCAPHARCA INAEQUIVALVIS
	Organism Taxid	:	6561
	Other Details	:	BLOOD CLAM
	Strain	:	SCAPHARCA INAEQUIVALVIS
	Synonym	:	GLOBIN II A CHAIN, HBII-A

Molecule 2 - HEMOGLOBIN B CHAIN
	Chains	:	B, D, F, H
	Organism Common	:	INEQUIVALVE ARK
	Organism Scientific	:	SCAPHARCA INAEQUIVALVIS
	Organism Taxid	:	6561
	Other Details	:	BLOOD CLAM
	Strain	:	SCAPHARCA INAEQUIVALVIS

		1	2	3	4	5	6	7	8
Asymmetric Unit	:	A	B	C	D	E	F	G	H
Biological Unit 1 (1x)	:	A	B	C	D
Biological Unit 2 (1x)	:					E	F	G	H

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 15)

No.	Name	Count	Type	Full Name
1	ACE	6	Mod. Amino Acid	ACETYL GROUP
2	HEM	8	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (2, 7)

No.	Name	Count	Type	Full Name
1	ACE	3	Mod. Amino Acid	ACETYL GROUP
2	HEM	4	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	PO4	-1	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (3, 8)

No.	Name	Count	Type	Full Name
1	ACE	3	Mod. Amino Acid	ACETYL GROUP
2	HEM	4	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	PO4	1	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:50 , PHE A:51 , ARG A:53 , HIS A:69 , LEU A:73 , LEU A:77 , PHE A:97 , ASN A:100 , HIS A:101 , ARG A:104 , ILE A:106 , PHE A:111 , HOH A:314 , HOH A:321 , HOH A:456 , HOH A:521 , HOH A:557 , LYS B:98 , ASN B:102	BINDING SITE FOR RESIDUE HEM A 201
2	AC2	SOFTWARE	LYS A:96 , ASN A:100 , LYS B:52 , PHE B:53 , ARG B:55 , HIS B:71 , LEU B:75 , PHE B:99 , ASN B:102 , HIS B:103 , ARG B:106 , ILE B:108 , PHE B:113 , HOH B:321 , HOH B:336 , HOH B:415 , HOH B:492	BINDING SITE FOR RESIDUE HEM B 201
3	AC3	SOFTWARE	TYR C:50 , PHE C:51 , ARG C:53 , HIS C:69 , LEU C:73 , PHE C:97 , ASN C:100 , HIS C:101 , ARG C:104 , ILE C:106 , PHE C:111 , HOH C:350 , HOH C:351 , HOH C:469 , HOH C:533 , HOH C:535 , LYS D:98 , ASN D:102	BINDING SITE FOR RESIDUE HEM C 201
4	AC4	SOFTWARE	LYS C:96 , ASN C:100 , LYS D:52 , PHE D:53 , ARG D:55 , HIS D:71 , LEU D:75 , PHE D:99 , ASN D:102 , HIS D:103 , ARG D:106 , ILE D:108 , PHE D:113 , HOH D:314 , HOH D:359 , HOH D:379	BINDING SITE FOR RESIDUE HEM D 201
5	AC5	SOFTWARE	TYR E:50 , PHE E:51 , ARG E:53 , LEU E:54 , HIS E:69 , LEU E:73 , PHE E:97 , ASN E:100 , HIS E:101 , ARG E:104 , ILE E:106 , PHE E:111 , HOH E:316 , HOH E:360 , HOH E:459 , HOH E:469 , HOH E:522 , LYS F:98 , ASN F:102	BINDING SITE FOR RESIDUE HEM E 201
6	AC6	SOFTWARE	LYS E:7 , HOH E:320 , ARG H:127 , HOH H:315	BINDING SITE FOR RESIDUE PO4 E 202
7	AC7	SOFTWARE	LYS E:96 , ASN E:100 , LYS F:52 , PHE F:53 , ARG F:55 , LEU F:56 , HIS F:71 , LEU F:75 , PHE F:99 , ASN F:102 , HIS F:103 , ARG F:106 , ILE F:108 , PHE F:113 , HOH F:301 , HOH F:327 , HOH F:366	BINDING SITE FOR RESIDUE HEM F 201
8	AC8	SOFTWARE	TYR G:50 , PHE G:51 , ARG G:53 , HIS G:69 , LEU G:73 , LEU G:77 , PHE G:97 , ASN G:100 , HIS G:101 , ARG G:104 , ILE G:106 , PHE G:111 , HOH G:342 , HOH G:380 , HOH G:412 , LYS H:98 , ASN H:102	BINDING SITE FOR RESIDUE HEM G 201
9	AC9	SOFTWARE	LYS G:96 , ASN G:100 , LYS H:52 , PHE H:53 , ARG H:55 , LEU H:56 , HIS H:71 , LEU H:75 , PHE H:99 , ASN H:102 , HIS H:103 , ARG H:106 , PHE H:113 , GLU H:115 , HOH H:321 , HOH H:341 , HOH H:351 , HOH H:361	BINDING SITE FOR RESIDUE HEM H 201

(no "SS Bond" information available for 4HRT)

(no "Cis Peptide Bond" information available for 4HRT)

(no "SAP(SNP)/Variant" information available for 4HRT)

(no "PROSITE Motif" information available for 4HRT)

(no "Exon" information available for 4HRT)

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:150
                                                                                                                                                                                      
               SCOP domains d4hrta_ A: Hemoglobin I                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4hrt A   0 xVDAAVAKVCGSEAIKANLRRSWGVLSADIEATGLMLMSNLFTLRPDTKTYFTRLGDVQKGKANSKLRGHAITLTYALNNFVDSLDDPSRLKCVVEKFAVNHINRKISGDAFGAIVEPMKETLKARMGNYYSDDVAGAWAALVGVVQAAL 149
                            |        9        19        29        39        49        59        69        79        89        99       109       119       129       139       149
                            |                                                                                                                                                     
                            0-ACE

Chain B from PDB  Type:PROTEIN  Length:147
                                                                                                                                                                                   
               SCOP domains d4hrtb_ B: automated matches                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hrt B   2 RVAELANAVVSNADQKDLLRMSWGVLSVDMEGTGLMLMANLFKTSPSAKGKFARLGDVSDNSKLRGHSITLMYALQNFVDALDDVERLKCVVEKFAVNHINRQISADEFGEIVGPLRQTLKARMGNYFDEDTVAAWASLVAVVQAAL 151
                                    11        21        31        41        51        64        74        84        94       104       114       124       134       144       
                                                                                     60|                                                                                       
                                                                                      64

Chain C from PDB  Type:PROTEIN  Length:150
                                                                                                                                                                                      
               SCOP domains d4hrtc_ C: Hemoglobin I                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4hrt C   0 xVDAAVAKVCGSEAIKANLRRSWGVLSADIEATGLMLMSNLFTLRPDTKTYFTRLGDVQKGKANSKLRGHAITLTYALNNFVDSLDDPSRLKCVVEKFAVNHINRKISGDAFGAIVEPMKETLKARMGNYYSDDVAGAWAALVGVVQAAL 149
                            |        9        19        29        39        49        59        69        79        89        99       109       119       129       139       149
                            0-ACE

Chain D from PDB  Type:PROTEIN  Length:152
                                                                                                                                                                                        
               SCOP domains d4hrtd_ D: automated matches                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hrt D   0 xSRVAELANAVVSNADQKDLLRMSWGVLSVDMEGTGLMLMANLFKTSPSAKGKFARLGDVSAGKDNSKLRGHSITLMYALQNFVDALDDVERLKCVVEKFAVNHINRQISADEFGEIVGPLRQTLKARMGNYFDEDTVAAWASLVAVVQAAL 151
                            |        9        19        29        39        49        59        69        79        89        99       109       119       129       139       149  
                            0-ACE

Chain E from PDB  Type:PROTEIN  Length:150
                                                                                                                                                                                      
               SCOP domains d4hrte_ E: Hemoglobin I                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4hrt E   0 xVDAAVAKVCGSEAIKANLRRSWGVLSADIEATGLMLMSNLFTLRPDTKTYFTRLGDVQKGKANSKLRGHAITLTYALNNFVDSLDDPSRLKCVVEKFAVNHINRKISGDAFGAIVEPMKETLKARMGNYYSDDVAGAWAALVGVVQAAL 149
                            |        9        19        29        39        49        59        69        79        89        99       109       119       129       139       149
                            0-ACE

Chain F from PDB  Type:PROTEIN  Length:151
                                                                                                                                                                                       
               SCOP domains d4hrtf_ F: automated matches                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hrt F   1 SRVAELANAVVSNADQKDLLRMSWGVLSVDMEGTGLMLMANLFKTSPSAKGKFARLGDVSAGKDNSKLRGHSITLMYALQNFVDALDDVERLKCVVEKFAVNHINRQISADEFGEIVGPLRQTLKARMGNYFDEDTVAAWASLVAVVQAAL 151
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain G from PDB  Type:PROTEIN  Length:150
                                                                                                                                                                                      
               SCOP domains d4hrtg_ G: Hemoglobin I                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4hrt G   0 xVDAAVAKVCGSEAIKANLRRSWGVLSADIEATGLMLMSNLFTLRPDTKTYFTRLGDVQKGKANSKLRGHAITLTYALNNFVDSLDDPSRLKCVVEKFAVNHINRKISGDAFGAIVEPMKETLKARMGNYYSDDVAGAWAALVGVVQAAL 149
                            |        9        19        29        39        49        59        69        79        89        99       109       119       129       139       149
                            0-ACE

Chain H from PDB  Type:PROTEIN  Length:149
                                                                                                                                                                                     
               SCOP domains d4hrth_ H: automated matches                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hrt H   0 xSRVAELANAVVSNADQKDLLRMSWGVLSVDMEGTGLMLMANLFKTSPSAKGKFARLGDVSDNSKLRGHSITLMYALQNFVDALDDVERLKCVVEKFAVNHINRQISADEFGEIVGPLRQTLKARMGNYFDEDTVAAWASLVAVVQAAL 151
                            |        9        19        29        39        49        59||      72        82        92       102       112       122       132       142         
                            0-ACE                                                      60|                                                                                       
                                                                                        64

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: Globins (1157)

Protein domain: automated matches (99)

Ark clam (Scapharca inaequivalvis) [TaxId: 6561] (31)

1a	d4hrtb_	B:
1b	d4hrtd_	D:
1c	d4hrtf_	F:
1d	d4hrth_	H:

Protein domain: Hemoglobin I (40)

Ark clam (Scapharca inaequivalvis) [TaxId: 6561] (36)

2a	d4hrta_	A:
2b	d4hrtc_	C:
2c	d4hrte_	E:
2d	d4hrtg_	G:

(no "CATH Domain" information available for 4HRT)

(no "Pfam Domain" information available for 4HRT)

Asymmetric Unit(hide GO term definitions)

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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4hrt)

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4hrr	SCAPHARCA TETRAMERIC HEMOGLOBIN, CO LIGANDED

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 15)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (2, 8)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File