1HMO - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   THE STRUCTURE OF DEOXY AND OXY HEMERYTHRIN AT 2.0 ANGSTROMS RESOLUTION

Authors :   M. A. Holmes, I. Letrong, S. Turley, L. C. Sieker, R. E. Stenkamp

Date :   18 Oct 90 (Deposition) - 15 Jan 92 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

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

Reference :   M. A. Holmes, I. Le Trong, S. Turley, L. C. Sieker, R. E. Stenkamp
Structures Of Deoxy And Oxy Hemerythrin At 2. 0 A Resolution
J. Mol. Biol. V. 218 583 1991
PubMed-ID: 2016748 | Reference-DOI: 10.1016/0022-2836(91)90703-9
(for further references see the PDB file header)

Molecule 1 - HEMERYTHRIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Organism Scientific	:	THEMISTE DYSCRITUM
	Organism Taxid	:	6436

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 12)

No.	Name	Count	Type	Full Name
1	ACE	4	Mod. Amino Acid	ACETYL GROUP
2	FEO	4	Ligand/Ion	MU-OXO-DIIRON
3	OXY	4	Ligand/Ion	OXYGEN MOLECULE

Biological Unit 1 (3, 24)

No.	Name	Count	Type	Full Name
1	ACE	8	Mod. Amino Acid	ACETYL GROUP
2	FEO	8	Ligand/Ion	MU-OXO-DIIRON
3	OXY	8	Ligand/Ion	OXYGEN MOLECULE

Biological Unit 2 (3, 6)

No.	Name	Count	Type	Full Name
1	ACE	2	Mod. Amino Acid	ACETYL GROUP
2	FEO	2	Ligand/Ion	MU-OXO-DIIRON
3	OXY	2	Ligand/Ion	OXYGEN MOLECULE

Biological Unit 3 (3, 24)

No.	Name	Count	Type	Full Name
1	ACE	8	Mod. Amino Acid	ACETYL GROUP
2	FEO	8	Ligand/Ion	MU-OXO-DIIRON
3	OXY	8	Ligand/Ion	OXYGEN MOLECULE

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLN A:60 , SER A:64	BINDING SITE FOR RESIDUE ACE A 114
02	AC2	SOFTWARE	HIS A:25 , HIS A:54 , GLU A:58 , HIS A:73 , HIS A:77 , HIS A:101 , ASP A:106 , OXY A:116	BINDING SITE FOR RESIDUE FEO A 115
03	AC3	SOFTWARE	HIS A:25 , HIS A:54 , PHE A:55 , LEU A:98 , HIS A:101 , ASP A:106 , FEO A:115	BINDING SITE FOR RESIDUE OXY A 116
04	AC4	SOFTWARE	SER B:64 , HOH B:158 , HOH B:179	BINDING SITE FOR RESIDUE ACE B 114
05	AC5	SOFTWARE	HIS B:25 , HIS B:54 , GLU B:58 , HIS B:73 , HIS B:77 , HIS B:101 , ASP B:106 , OXY B:116	BINDING SITE FOR RESIDUE FEO B 115
06	AC6	SOFTWARE	HIS B:25 , LEU B:28 , HIS B:54 , PHE B:55 , LEU B:98 , HIS B:101 , ILE B:102 , ASP B:106 , FEO B:115	BINDING SITE FOR RESIDUE OXY B 116
07	AC7	SOFTWARE	SER C:64 , HOH C:195	BINDING SITE FOR RESIDUE ACE C 114
08	AC8	SOFTWARE	HIS C:25 , HIS C:54 , GLU C:58 , HIS C:73 , HIS C:77 , HIS C:101 , ASP C:106 , OXY C:116	BINDING SITE FOR RESIDUE FEO C 115
09	AC9	SOFTWARE	HIS C:25 , HIS C:54 , PHE C:55 , LEU C:98 , HIS C:101 , ILE C:102 , ASP C:106 , FEO C:115	BINDING SITE FOR RESIDUE OXY C 116
10	BC1	SOFTWARE	GLN D:60 , SER D:64 , HOH D:282	BINDING SITE FOR RESIDUE ACE D 114
11	BC2	SOFTWARE	HIS D:25 , HIS D:54 , GLU D:58 , HIS D:73 , HIS D:77 , HIS D:101 , ASP D:106 , OXY D:116	BINDING SITE FOR RESIDUE FEO D 115
12	BC3	SOFTWARE	HIS D:25 , HIS D:54 , PHE D:55 , LEU D:98 , HIS D:101 , ILE D:102 , ASP D:106 , FEO D:115	BINDING SITE FOR RESIDUE OXY D 116

Asymmetric Unit

No.	Residues
1	A:9	-	B:9
2	C:9	-	D:9

Asymmetric 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

Asymmetric Unit (1, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_HEMT_THEDY_001 *	A	64	S	HEMT_THEDY	---	---	A/B/C/D	S	64	S
	* ID not provided by source

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

Biological Unit 1 (1, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_HEMT_THEDY_001 *	A	64	S	HEMT_THEDY	---	---	A/B	S	64	S
	* ID not provided by source

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

Biological Unit 2 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_HEMT_THEDY_001 *	A	64	S	HEMT_THEDY	---	---	C/D	S	64	S
	* ID not provided by source

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

Biological Unit 3 (1, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_HEMT_THEDY_001 *	A	64	S	HEMT_THEDY	---	---	C/D	S	64	S
	* ID not provided by source

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

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HEMERYTHRINS	PS00550	Hemerythrin family signature.	HEMT_THEDY	54-77	4	A:54-77 B:54-77 C:54-77 D:54-77

Biological Unit 1 (1, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HEMERYTHRINS	PS00550	Hemerythrin family signature.	HEMT_THEDY	54-77	8	A:54-77 B:54-77 - -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HEMERYTHRINS	PS00550	Hemerythrin family signature.	HEMT_THEDY	54-77	2	- - C:54-77 D:54-77

Biological Unit 3 (1, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HEMERYTHRINS	PS00550	Hemerythrin family signature.	HEMT_THEDY	54-77	8	- - C:54-77 D:54-77

(no "Exon" information available for 1HMO)

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:114
 aligned with HEMT_THEDY | P02246 from UniProtKB/Swiss-Prot  Length:113

    Alignment length:114
                                                                                                                                          113     
                                    10        20        30        40        50        60        70        80        90       100       110  | 
           HEMT_THEDY     1 GFPIPDPYCWDISFRTFYTIVDDEHKTLFNGILLLSQADNADHLNELRRCTGKHFLNEQQLMQASQYAGYAEHKKAHDDFIHKLDTWDGDVTYAKNWLVNHIKTIDFKYRGKI-   -
               SCOP domains d1hmoa_ A: Hemerythrin                                                                                             SCOP domains
               CATH domains 1hmoA00 A:1-113  [code=1.20.120.50, no name defined]                                                             - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh......hhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------S-------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------HEMERYTHRINS            ------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 1hmo A   1 GFPIPDPYCWDISFRTFYTIIDDEHKTLFNGILLLSQADNADHLNELRRCTGKHFLNEQQLMQSSQYAGYAEHKKAHDDFIHKLDTWDGDVTYAKNWLVNHIKTIDFKYRGKIx 114
                                    10        20        30        40        50        60        70        80        90       100       110   |
                                                                                                                                           114-ACE

Chain B from PDB  Type:PROTEIN  Length:114
 aligned with HEMT_THEDY | P02246 from UniProtKB/Swiss-Prot  Length:113

    Alignment length:114
                                                                                                                                          113     
                                    10        20        30        40        50        60        70        80        90       100       110  | 
           HEMT_THEDY     1 GFPIPDPYCWDISFRTFYTIVDDEHKTLFNGILLLSQADNADHLNELRRCTGKHFLNEQQLMQASQYAGYAEHKKAHDDFIHKLDTWDGDVTYAKNWLVNHIKTIDFKYRGKI-   -
               SCOP domains d1hmob_ B: Hemerythrin                                                                                             SCOP domains
               CATH domains 1hmoB00 B:1-113  [code=1.20.120.50, no name defined]                                                             - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh......hhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------S-------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------HEMERYTHRINS            ------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 1hmo B   1 GFPIPDPYCWDISFRTFYTIIDDEHKTLFNGILLLSQADNADHLNELRRCTGKHFLNEQQLMQSSQYAGYAEHKKAHDDFIHKLDTWDGDVTYAKNWLVNHIKTIDFKYRGKIx 114
                                    10        20        30        40        50        60        70        80        90       100       110   |
                                                                                                                                           114-ACE

Chain C from PDB  Type:PROTEIN  Length:114
 aligned with HEMT_THEDY | P02246 from UniProtKB/Swiss-Prot  Length:113

    Alignment length:114
                                                                                                                                          113     
                                    10        20        30        40        50        60        70        80        90       100       110  | 
           HEMT_THEDY     1 GFPIPDPYCWDISFRTFYTIVDDEHKTLFNGILLLSQADNADHLNELRRCTGKHFLNEQQLMQASQYAGYAEHKKAHDDFIHKLDTWDGDVTYAKNWLVNHIKTIDFKYRGKI-   -
               SCOP domains d1hmoc_ C: Hemerythrin                                                                                             SCOP domains
               CATH domains 1hmoC00 C:1-113  [code=1.20.120.50, no name defined]                                                             - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh......hhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------S-------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------HEMERYTHRINS            ------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 1hmo C   1 GFPIPDPYCWDISFRTFYTIIDDEHKTLFNGILLLSQADNADHLNELRRCTGKHFLNEQQLMQSSQYAGYAEHKKAHDDFIHKLDTWDGDVTYAKNWLVNHIKTIDFKYRGKIx 114
                                    10        20        30        40        50        60        70        80        90       100       110   |
                                                                                                                                           114-ACE

Chain D from PDB  Type:PROTEIN  Length:114
 aligned with HEMT_THEDY | P02246 from UniProtKB/Swiss-Prot  Length:113

    Alignment length:114
                                                                                                                                          113     
                                    10        20        30        40        50        60        70        80        90       100       110  | 
           HEMT_THEDY     1 GFPIPDPYCWDISFRTFYTIVDDEHKTLFNGILLLSQADNADHLNELRRCTGKHFLNEQQLMQASQYAGYAEHKKAHDDFIHKLDTWDGDVTYAKNWLVNHIKTIDFKYRGKI-   -
               SCOP domains d1hmod_ D: Hemerythrin                                                                                             SCOP domains
               CATH domains 1hmoD00 D:1-113  [code=1.20.120.50, no name defined]                                                             - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh......hhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------S-------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------HEMERYTHRINS            ------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 1hmo D   1 GFPIPDPYCWDISFRTFYTIIDDEHKTLFNGILLLSQADNADHLNELRRCTGKHFLNEQQLMQSSQYAGYAEHKKAHDDFIHKLDTWDGDVTYAKNWLVNHIKTIDFKYRGKIx 114
                                    10        20        30        40        50        60        70        80        90       100       110   |
                                                                                                                                           114-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: Four-helical up-and-down bundle (308)

Superfamily: Hemerythrin-like (10)

Family: Hemerythrin-like (10)

Protein domain: Hemerythrin (7)

Sipunculid worm (Themiste dyscritum) [TaxId: 6436] (4)

1a	d1hmoa_	A:
1b	d1hmob_	B:
1c	d1hmoc_	C:
1d	d1hmod_	D:

Asymmetric 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)

Themiste dyscritum. Organism_taxid: 6436 (4)

1a	1hmoA00	A:1-113
1b	1hmoB00	B:1-113
1c	1hmoC00	C:1-113
1d	1hmoD00	D:1-113

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (HEMT_THEDY | P02246)

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 Unit
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Description

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Ligands, Modified Residues, Ions (3, 12)

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SS Bonds (2, 2)

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