1I4Z - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   THE CRYSTAL STRUCTURE OF PHASCOLOPSIS GOULDII L98Y METHEMERYTHRIN

Authors :   C. S. Farmer, D. M. Kurtz Jr. , Z. -J. Liu, B. C. Wang, J. Rose

Date :   23 Feb 01 (Deposition) - 21 Mar 01 (Release) - 25 Jul 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym./Biol. Unit : A,B,C,D,E,F,G,H

Keywords :   Hemerythrin, Oxygen Binding, Diiron, Mutation, Four-Helix Bundle, Oxygen Storage-Transport Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. S. Farmer, D. M. Kurtz Jr. , Z. J. Liu, B. C. Wang, J. Rose, J. Ai, J. Sanders-Loehr
The Crystal Structures Of Phascolopsis Gouldii Wild Type An L98Y Methemerythrins: Structural And Functional Alterations Of The O2 Binding Pocket.
J. Biol. Inorg. Chem. V. 6 418 2001
PubMed-ID: 11372200 | Reference-DOI: 10.1007/S007750100218

Molecule 1 - METHEMERYTHRIN
	Chains	:	A, B, C, D, E, F, G, H
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Mutation	:	YES
	Organism Scientific	:	PHASCOLOPSIS GOULDII
	Organism Taxid	:	6442
	Synonym	:	HEMERYTHRIN

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 8)

No.	Name	Count	Type	Full Name
1	FEO	8	Ligand/Ion	MU-OXO-DIIRON

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:25 , HIS A:54 , GLU A:58 , HIS A:73 , HIS A:77 , HIS A:101 , ASP A:106 , HOH A:625	BINDING SITE FOR RESIDUE FEO A 601
2	AC2	SOFTWARE	HIS B:25 , HIS B:54 , PHE B:55 , GLU B:58 , HIS B:73 , HIS B:77 , HIS B:101 , ASP B:106	BINDING SITE FOR RESIDUE FEO B 602
3	AC3	SOFTWARE	HIS C:25 , HIS C:54 , PHE C:55 , GLU C:58 , HIS C:73 , HIS C:77 , HIS C:101 , ASP C:106	BINDING SITE FOR RESIDUE FEO C 603
4	AC4	SOFTWARE	HIS D:25 , HIS D:54 , PHE D:55 , GLU D:58 , HIS D:73 , HIS D:77 , HIS D:101 , ASP D:106	BINDING SITE FOR RESIDUE FEO D 604
5	AC5	SOFTWARE	HIS E:25 , HIS E:54 , PHE E:55 , GLU E:58 , HIS E:73 , HIS E:77 , HIS E:101 , ASP E:106 , HOH E:621	BINDING SITE FOR RESIDUE FEO E 605
6	AC6	SOFTWARE	HIS F:25 , HIS F:54 , GLU F:58 , HIS F:73 , HIS F:77 , HIS F:101 , ASP F:106 , HOH F:626	BINDING SITE FOR RESIDUE FEO F 606
7	AC7	SOFTWARE	HIS G:25 , HIS G:54 , GLU G:58 , HIS G:73 , HIS G:77 , HIS G:101 , ASP G:106	BINDING SITE FOR RESIDUE FEO G 607
8	AC8	SOFTWARE	HIS H:25 , HIS H:54 , PHE H:55 , GLU H:58 , HIS H:73 , HIS H:77 , HIS H:101 , ASP H:106	BINDING SITE FOR RESIDUE FEO H 608

(no "SS Bond" information available for 1I4Z)

Asymmetric/Biological Unit

No.	Residues
1	Asp A:6	-	Pro A:7
2	Asp B:6	-	Pro B:7
3	Asp C:6	-	Pro C:7
4	Asp D:6	-	Pro D:7
5	Asp E:6	-	Pro E:7
6	Asp F:6	-	Pro F:7
7	Asp G:6	-	Pro G:7
8	Asp H:6	-	Pro H:7

Asymmetric/Biological Unit (5, 40)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_HEMT_PHAGO_001 *	Q	64	E	HEMT_PHAGO	---	---	A/B/C/D/E/F/G/H	Q	63	E
2	UniProt	VAR_HEMT_PHAGO_002 *	E	79	D	HEMT_PHAGO	---	---	A/B/C/D/E/F/G/H	E	78	D
3	UniProt	VAR_HEMT_PHAGO_003 *	T	80	G	HEMT_PHAGO	---	---	A/B/C/D/E/F/G/H	T	79	G
4	UniProt	VAR_HEMT_PHAGO_004 *	H	83	N	HEMT_PHAGO	---	---	A/B/C/D/E/F/G/H	H	82	N
5	UniProt	VAR_HEMT_PHAGO_005 *	S	97	A	HEMT_PHAGO	---	---	A/B/C/D/E/F/G/H	S	96	A
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (1, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HEMERYTHRINS	PS00550	Hemerythrin family signature.	HEMT_PHAGO	55-78	8	A:54-77 B:54-77 C:54-77 D:54-77 E:54-77 F:54-77 G:54-77 H:54-77

(no "Exon" information available for 1I4Z)

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:113
 aligned with HEMT_PHAGO | P02244 from UniProtKB/Swiss-Prot  Length:114

    Alignment length:113
                                    11        21        31        41        51        61        71        81        91       101       111   
           HEMT_PHAGO     2 GFPIPDPYVWDPSFRTFYSIIDDEHKTLFNGIFHLAIDDNADNLGELRRCTGKHFLNEQVLMQASQYQFYDEHKKEHETFIHALDNWKGDVKWAKSWLVNHIKTIDFKYKGKI 114
               SCOP domains d1i4za_ A: Hemerythrin                                                                                            SCOP domains
               CATH domains 1i4zA00 A:1-113  [code=1.20.120.50, no name defined]                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------E--------------DG--N-------------A----------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------HEMERYTHRINS            ------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 1i4z A   1 GFPIPDPYVWDPSFRTFYSIIDDEHKTLFNGIFHLAIDDNADNLGELRRCTGKHFLNEQVLMQASQYQFYDEHKKEHETFIHALDNWKGDVKWAKSWYVNHIKTIDFKYKGKI 113
                                    10        20        30        40        50        60        70        80        90       100       110

Chain B from PDB  Type:PROTEIN  Length:113
 aligned with HEMT_PHAGO | P02244 from UniProtKB/Swiss-Prot  Length:114

    Alignment length:113
                                    11        21        31        41        51        61        71        81        91       101       111   
           HEMT_PHAGO     2 GFPIPDPYVWDPSFRTFYSIIDDEHKTLFNGIFHLAIDDNADNLGELRRCTGKHFLNEQVLMQASQYQFYDEHKKEHETFIHALDNWKGDVKWAKSWLVNHIKTIDFKYKGKI 114
               SCOP domains d1i4zb_ B: Hemerythrin                                                                                            SCOP domains
               CATH domains 1i4zB00 B:1-113  [code=1.20.120.50, no name defined]                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------E--------------DG--N-------------A----------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------HEMERYTHRINS            ------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 1i4z B   1 GFPIPDPYVWDPSFRTFYSIIDDEHKTLFNGIFHLAIDDNADNLGELRRCTGKHFLNEQVLMQASQYQFYDEHKKEHETFIHALDNWKGDVKWAKSWYVNHIKTIDFKYKGKI 113
                                    10        20        30        40        50        60        70        80        90       100       110

Chain C from PDB  Type:PROTEIN  Length:113
 aligned with HEMT_PHAGO | P02244 from UniProtKB/Swiss-Prot  Length:114

    Alignment length:113
                                    11        21        31        41        51        61        71        81        91       101       111   
           HEMT_PHAGO     2 GFPIPDPYVWDPSFRTFYSIIDDEHKTLFNGIFHLAIDDNADNLGELRRCTGKHFLNEQVLMQASQYQFYDEHKKEHETFIHALDNWKGDVKWAKSWLVNHIKTIDFKYKGKI 114
               SCOP domains d1i4zc_ C: Hemerythrin                                                                                            SCOP domains
               CATH domains 1i4zC00 C:1-113  [code=1.20.120.50, no name defined]                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------E--------------DG--N-------------A----------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------HEMERYTHRINS            ------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 1i4z C   1 GFPIPDPYVWDPSFRTFYSIIDDEHKTLFNGIFHLAIDDNADNLGELRRCTGKHFLNEQVLMQASQYQFYDEHKKEHETFIHALDNWKGDVKWAKSWYVNHIKTIDFKYKGKI 113
                                    10        20        30        40        50        60        70        80        90       100       110

Chain D from PDB  Type:PROTEIN  Length:113
 aligned with HEMT_PHAGO | P02244 from UniProtKB/Swiss-Prot  Length:114

    Alignment length:113
                                    11        21        31        41        51        61        71        81        91       101       111   
           HEMT_PHAGO     2 GFPIPDPYVWDPSFRTFYSIIDDEHKTLFNGIFHLAIDDNADNLGELRRCTGKHFLNEQVLMQASQYQFYDEHKKEHETFIHALDNWKGDVKWAKSWLVNHIKTIDFKYKGKI 114
               SCOP domains d1i4zd_ D: Hemerythrin                                                                                            SCOP domains
               CATH domains 1i4zD00 D:1-113  [code=1.20.120.50, no name defined]                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------E--------------DG--N-------------A----------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------HEMERYTHRINS            ------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 1i4z D   1 GFPIPDPYVWDPSFRTFYSIIDDEHKTLFNGIFHLAIDDNADNLGELRRCTGKHFLNEQVLMQASQYQFYDEHKKEHETFIHALDNWKGDVKWAKSWYVNHIKTIDFKYKGKI 113
                                    10        20        30        40        50        60        70        80        90       100       110

Chain E from PDB  Type:PROTEIN  Length:113
 aligned with HEMT_PHAGO | P02244 from UniProtKB/Swiss-Prot  Length:114

    Alignment length:113
                                    11        21        31        41        51        61        71        81        91       101       111   
           HEMT_PHAGO     2 GFPIPDPYVWDPSFRTFYSIIDDEHKTLFNGIFHLAIDDNADNLGELRRCTGKHFLNEQVLMQASQYQFYDEHKKEHETFIHALDNWKGDVKWAKSWLVNHIKTIDFKYKGKI 114
               SCOP domains d1i4ze_ E: Hemerythrin                                                                                            SCOP domains
               CATH domains 1i4zE00 E:1-113  [code=1.20.120.50, no name defined]                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------E--------------DG--N-------------A----------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------HEMERYTHRINS            ------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 1i4z E   1 GFPIPDPYVWDPSFRTFYSIIDDEHKTLFNGIFHLAIDDNADNLGELRRCTGKHFLNEQVLMQASQYQFYDEHKKEHETFIHALDNWKGDVKWAKSWYVNHIKTIDFKYKGKI 113
                                    10        20        30        40        50        60        70        80        90       100       110

Chain F from PDB  Type:PROTEIN  Length:113
 aligned with HEMT_PHAGO | P02244 from UniProtKB/Swiss-Prot  Length:114

    Alignment length:113
                                    11        21        31        41        51        61        71        81        91       101       111   
           HEMT_PHAGO     2 GFPIPDPYVWDPSFRTFYSIIDDEHKTLFNGIFHLAIDDNADNLGELRRCTGKHFLNEQVLMQASQYQFYDEHKKEHETFIHALDNWKGDVKWAKSWLVNHIKTIDFKYKGKI 114
               SCOP domains d1i4zf_ F: Hemerythrin                                                                                            SCOP domains
               CATH domains 1i4zF00 F:1-113  [code=1.20.120.50, no name defined]                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------E--------------DG--N-------------A----------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------HEMERYTHRINS            ------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 1i4z F   1 GFPIPDPYVWDPSFRTFYSIIDDEHKTLFNGIFHLAIDDNADNLGELRRCTGKHFLNEQVLMQASQYQFYDEHKKEHETFIHALDNWKGDVKWAKSWYVNHIKTIDFKYKGKI 113
                                    10        20        30        40        50        60        70        80        90       100       110

Chain G from PDB  Type:PROTEIN  Length:113
 aligned with HEMT_PHAGO | P02244 from UniProtKB/Swiss-Prot  Length:114

    Alignment length:113
                                    11        21        31        41        51        61        71        81        91       101       111   
           HEMT_PHAGO     2 GFPIPDPYVWDPSFRTFYSIIDDEHKTLFNGIFHLAIDDNADNLGELRRCTGKHFLNEQVLMQASQYQFYDEHKKEHETFIHALDNWKGDVKWAKSWLVNHIKTIDFKYKGKI 114
               SCOP domains d1i4zg_ G: Hemerythrin                                                                                            SCOP domains
               CATH domains 1i4zG00 G:1-113  [code=1.20.120.50, no name defined]                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------E--------------DG--N-------------A----------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------HEMERYTHRINS            ------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 1i4z G   1 GFPIPDPYVWDPSFRTFYSIIDDEHKTLFNGIFHLAIDDNADNLGELRRCTGKHFLNEQVLMQASQYQFYDEHKKEHETFIHALDNWKGDVKWAKSWYVNHIKTIDFKYKGKI 113
                                    10        20        30        40        50        60        70        80        90       100       110

Chain H from PDB  Type:PROTEIN  Length:113
 aligned with HEMT_PHAGO | P02244 from UniProtKB/Swiss-Prot  Length:114

    Alignment length:113
                                    11        21        31        41        51        61        71        81        91       101       111   
           HEMT_PHAGO     2 GFPIPDPYVWDPSFRTFYSIIDDEHKTLFNGIFHLAIDDNADNLGELRRCTGKHFLNEQVLMQASQYQFYDEHKKEHETFIHALDNWKGDVKWAKSWLVNHIKTIDFKYKGKI 114
               SCOP domains d1i4zh_ H: Hemerythrin                                                                                            SCOP domains
               CATH domains 1i4zH00 H:1-113  [code=1.20.120.50, no name defined]                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------E--------------DG--N-------------A----------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------HEMERYTHRINS            ------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 1i4z H   1 GFPIPDPYVWDPSFRTFYSIIDDEHKTLFNGIFHLAIDDNADNLGELRRCTGKHFLNEQVLMQASQYQFYDEHKKEHETFIHALDNWKGDVKWAKSWYVNHIKTIDFKYKGKI 113
                                    10        20        30        40        50        60        70        80        90       100       110

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: Four-helical up-and-down bundle (308)

Superfamily: Hemerythrin-like (10)

Family: Hemerythrin-like (10)

Protein domain: Hemerythrin (7)

Phascolopsis gouldii [TaxId: 6442] (3)

1a	d1i4za_	A:
1b	d1i4zc_	C:
1c	d1i4zd_	D:
1d	d1i4ze_	E:
1e	d1i4zf_	F:
1f	d1i4zg_	G:
1g	d1i4zh_	H:
1h	d1i4zb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Four Helix Bundle (Hemerythrin (Met), subunit A) (300)

Homologous Superfamily: [code=1.20.120.50, no name defined] (10)

Phascolopsis gouldii. Organism_taxid: 6442. (2)

1a	1i4zA00	A:1-113
1b	1i4zC00	C:1-113
1c	1i4zD00	D:1-113
1d	1i4zE00	E:1-113
1e	1i4zF00	F:1-113
1f	1i4zG00	G:1-113
1g	1i4zH00	H:1-113
1h	1i4zB00	B:1-113

(no "Pfam Domain" information available for 1I4Z)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D,E,F,G,H (HEMT_PHAGO | P02244)

molecular function
	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: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.

Asymmetric/Biological Unit
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	HEMT_PHAGO \| P02244	:	1hrb 1i4y

1i4y	PHASCOLOPSIS GOULDII WILD TYPE METHEMERYTHRIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (5, 40)

PROSITE Motifs (1, 8)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 8)

CATH Domains (1, 8)

Pfam Domains (0, 0)

Gene Ontology (5, 5)

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Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File