1HMD - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asym.Unit - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

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 (2, 8)

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

Biological Unit 1 (2, 16)

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

Biological Unit 2 (2, 4)

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

Biological Unit 3 (2, 16)

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

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:60 , SER A:64	BINDING SITE FOR RESIDUE ACE A 114
2	AC2	SOFTWARE	HIS A:25 , HIS A:54 , GLU A:58 , HIS A:73 , HIS A:77 , HIS A:101 , ASP A:106 , HOH A:135	BINDING SITE FOR RESIDUE FEO A 115
3	AC3	SOFTWARE	SER B:64 , HOH B:185	BINDING SITE FOR RESIDUE ACE B 114
4	AC4	SOFTWARE	HIS B:25 , HIS B:54 , GLU B:58 , HIS B:73 , HIS B:77 , HIS B:101 , ASP B:106	BINDING SITE FOR RESIDUE FEO B 115
5	AC5	SOFTWARE	SER C:64 , HOH C:211	BINDING SITE FOR RESIDUE ACE C 114
6	AC6	SOFTWARE	HIS C:25 , HIS C:54 , GLU C:58 , HIS C:73 , HIS C:77 , HIS C:101 , ASP C:106 , HOH C:147	BINDING SITE FOR RESIDUE FEO C 115
7	AC7	SOFTWARE	GLN D:60 , SER D:64 , HOH D:293	BINDING SITE FOR RESIDUE ACE D 114
8	AC8	SOFTWARE	HIS D:25 , HIS D:54 , GLU D:58 , HIS D:73 , HIS D:77 , HIS D:101 , ASP D:106	BINDING SITE FOR RESIDUE FEO D 115

Asymmetric Unit

No.	Residues
1	A:9	-	B: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 1HMD)

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 d1hmda_ A: Hemerythrin                                                                                             SCOP domains
               CATH domains 1hmdA00 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
                 1hmd 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 d1hmdb_ B: Hemerythrin                                                                                             SCOP domains
               CATH domains 1hmdB00 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
                 1hmd 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 d1hmdc_ C: Hemerythrin                                                                                             SCOP domains
               CATH domains 1hmdC00 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
                 1hmd 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 d1hmdd_ D: Hemerythrin                                                                                             SCOP domains
               CATH domains 1hmdD00 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
                 1hmd 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	d1hmda_	A:
1b	d1hmdc_	C:
1c	d1hmdd_	D:
1d	d1hmdb_	B:

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	1hmdA00	A:1-113
1b	1hmdC00	C:1-113
1c	1hmdD00	D:1-113
1d	1hmdB00	B:1-113

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

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
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		ACE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		FEO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Asp A:6 - Pro A:7	[ RasMol ]
		Asp B:6 - Pro B:7	[ RasMol ]
		Asp C:6 - Pro C:7	[ RasMol ]
		Asp D:6 - Pro D:7	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format \| Biol. Unit 3 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1hmd
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	HEMT_THEDY \| P02246
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	HEMT_THEDY \| P02246
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	HEMT_THEDY \| P02246	:	1hmo 2hmq 2hmz

(no "Related Entries Specified in the PDB File" available for 1HMD)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

SS Bonds (1, 1)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 4)

PROSITE Motifs (1, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (1, 4)

Pfam Domains (0, 0)

Gene Ontology (5, 5)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File