1JMB - JenaLib

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)

Title :   CRYSTAL STRUCTURE OF FOUR-HELIX BUNDLE MODEL

Authors :   L. Di Costanzo, S. Geremia

Date :   18 Jul 01 (Deposition) - 16 Jan 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Alpha-Helical Bundle, Protein Design, De Novo Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Di Costanzo, H. Wade, S. Geremia, L. Randaccio, V. Pavone, W. F. Degrado, A. Lombardi
Toward The De Novo Design Of A Catalytically Active Helix Bundle: A Substrate-Accessible Carboxylate-Bridged Dinuclear Metal Center.
J. Am. Chem. Soc. V. 123 12749 2001
PubMed-ID: 11749531 | Reference-DOI: 10.1021/JA010506X
(for further references see the PDB file header)

Molecule 1 - PROTEIN (FOUR-HELIX BUNDLE MODEL)
	Chains	:	A, B, C
	Engineered	:	YES
	Other Details	:	THIS PROTEIN WAS CHEMICALLY SYNTHESIZED
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 11)

No.	Name	Count	Type	Full Name
1	ACE	3	Mod. Amino Acid	ACETYL GROUP
2	DMS	2	Ligand/Ion	DIMETHYL SULFOXIDE
3	MN	3	Ligand/Ion	MANGANESE (II) ION
4	NH2	3	Mod. Amino Acid	AMINO GROUP

Biological Unit 1 (3, 6)

No.	Name	Count	Type	Full Name
1	ACE	2	Mod. Amino Acid	ACETYL GROUP
2	DMS	2	Ligand/Ion	DIMETHYL SULFOXIDE
3	MN	-1	Ligand/Ion	MANGANESE (II) ION
4	NH2	2	Mod. Amino Acid	AMINO GROUP

Biological Unit 2 (3, 5)

No.	Name	Count	Type	Full Name
1	ACE	2	Mod. Amino Acid	ACETYL GROUP
2	DMS	1	Ligand/Ion	DIMETHYL SULFOXIDE
3	MN	-1	Ligand/Ion	MANGANESE (II) ION
4	NH2	2	Mod. Amino Acid	AMINO GROUP

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:10 , GLU A:36 , HIS A:39 , DMS A:302	BINDING SITE FOR RESIDUE MN A 401
2	AC2	SOFTWARE	GLU B:10 , GLU B:36 , HIS B:39 , DMS B:301 , GLU C:36	BINDING SITE FOR RESIDUE MN B 402
3	AC3	SOFTWARE	GLU B:36 , DMS B:301 , GLU C:10 , GLU C:36 , HIS C:39	BINDING SITE FOR RESIDUE MN C 403
4	AC4	SOFTWARE	LEU B:9 , GLU B:10 , ALA B:13 , GLU B:36 , MN B:402 , GLU C:10 , ALA C:13 , GLU C:36 , MN C:403	BINDING SITE FOR RESIDUE DMS B 301
5	AC5	SOFTWARE	LEU A:9 , GLU A:10 , ALA A:13 , GLU A:36 , MN A:401	BINDING SITE FOR RESIDUE DMS A 302

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

(no "Cis Peptide Bond" information available for 1JMB)

(no "SAP(SNP)/Variant" information available for 1JMB)

(no "PROSITE Motif" information available for 1JMB)

(no "Exon" information available for 1JMB)

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:50
                                                                                 
               SCOP domains d1jmba_ A: Artificial diiron protein               SCOP domains
               CATH domains -1jmbA00 A:1-48 Immunoglobulin FC, subunit C     - CATH domains
               Pfam domains -------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------- Transcript
                  1jmb A  0 xDYLRELLKLELQAIKQYREALEYVKLPVLAKILEDEEKHIEWLETILGx 49
                            |        9        19        29        39        49
                            |                                               49-NH2
                            0-ACE

Chain B from PDB  Type:PROTEIN  Length:50
                                                                                 
               SCOP domains d1jmbb_ B: Artificial diiron protein               SCOP domains
               CATH domains -1jmbB00 B:1-48 Immunoglobulin FC, subunit C     - CATH domains
               Pfam domains -------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------- Transcript
                  1jmb B  0 xDYLRELLKLELQAIKQYREALEYVKLPVLAKILEDEEKHIEWLETILGx 49
                            |        9        19        29        39        49
                            |                                               49-NH2
                            0-ACE

Chain C from PDB  Type:PROTEIN  Length:50
                                                                                 
               SCOP domains d1jmbc_ C: Artificial diiron protein               SCOP domains
               CATH domains -1jmbC00 C:1-48 Immunoglobulin FC, subunit C     - CATH domains
               Pfam domains -------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------- Transcript
                  1jmb C  0 xDYLRELLKLELQAIKQYREALEYVKLPVLAKILEDEEKHIEWLETILGx 49
                            |        9        19        29        39        49
                            |                                               49-NH2
                            0-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: Designed proteins (167)

Fold: Designed four-helix bundle protein (16)

Superfamily: Designed four-helix bundle protein (16)

Family: Designed four-helix bundle protein (16)

Protein domain: Artificial diiron protein (12)

Synthetic, different variants (12)

1a	d1jmba_	A:
1b	d1jmbb_	B:
1c	d1jmbc_	C:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Single alpha-helices involved in coiled-coils or other helix-helix interfaces (552)

Homologous Superfamily: Immunoglobulin FC, subunit C (42)

[unclassified] (10)

1a	1jmbA00	A:1-48
1b	1jmbB00	B:1-48
1c	1jmbC00	C:1-48

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

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 1JMB)

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 ]
		DMS	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NH2	[ 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 ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1jmb)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ 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 ](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
	1jmb
		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
	(no 'UniProt ID/Accession number' available) \|
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProt

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
	(no 'UniProt ID/Accession number' available) \|
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT

(no "Entries Sharing at Least One Protein Chain" available for 1JMB)

1ec5	1EC5 IS THE ZINC DERIVATIVE WITH ALA13 RESIDUE MUTATED TO LEU
1jm0	1JM0 IS A DIFFERENT CRYSTALLINE FORM (S.G. P212121) OF THE SAME STRUCTURE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 11)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 3)

CATH Domains (1, 3)

Pfam Domains (0, 0)

Gene Ontology (0, 0)

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