1JM0 - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF FOUR-HELIX BUNDLE MODEL

Authors :   L. Di Costanzo, S. Geremia

Date :   17 Jul 01 (Deposition) - 16 Jan 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)
Biol. Unit 3: E,F  (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, D, E, F
	Engineered	:	YES
	Other Details	:	THIS PROTEIN WAS CHEMICALLY SYNTHESIZED
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 26)

No.	Name	Count	Type	Full Name
1	ACE	6	Mod. Amino Acid	ACETYL GROUP
2	DMS	3	Ligand/Ion	DIMETHYL SULFOXIDE
3	MN	11	Ligand/Ion	MANGANESE (II) ION
4	NH2	6	Mod. Amino Acid	AMINO GROUP

Biological Unit 1 (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

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

Biological Unit 3 (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 (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU A:10 , GLU A:36 , HIS A:39 , GLU B:36 , DMS B:301 , MN B:402	BINDING SITE FOR RESIDUE MN A 401
02	AC2	SOFTWARE	GLU A:36 , MN A:401 , GLU B:10 , GLU B:36 , HIS B:39 , DMS B:301	BINDING SITE FOR RESIDUE MN B 402
03	AC3	SOFTWARE	GLU C:10 , GLU C:36 , HIS C:39 , DMS C:302 , GLU D:36 , MN D:404	BINDING SITE FOR RESIDUE MN C 403
04	AC4	SOFTWARE	GLU C:36 , DMS C:302 , MN C:403 , GLU D:10 , GLU D:36 , HIS D:39	BINDING SITE FOR RESIDUE MN D 404
05	AC5	SOFTWARE	GLU E:10 , GLU E:36 , HIS E:39 , GLU F:36 , DMS F:303	BINDING SITE FOR RESIDUE MN E 405
06	AC6	SOFTWARE	GLU E:36 , GLU F:10 , GLU F:36 , HIS F:39 , DMS F:303	BINDING SITE FOR RESIDUE MN F 406
07	AC7	SOFTWARE	HOH C:506 , GLN D:16 , GLU D:19 , HOH D:505 , GLU F:34 , HOH F:407	BINDING SITE FOR RESIDUE MN D 501
08	AC8	SOFTWARE	GLU B:37 , HOH B:504 , GLU E:34 , GLU E:37 , HOH E:503	BINDING SITE FOR RESIDUE MN E 502
09	AC9	SOFTWARE	GLN B:16 , GLU B:19 , HOH B:505 , HOH B:506 , HOH B:507	BINDING SITE FOR RESIDUE MN B 503
10	BC1	SOFTWARE	GLU D:34 , GLU D:37 , HOH D:506 , HOH D:507 , HOH D:508	BINDING SITE FOR RESIDUE MN D 504
11	BC2	SOFTWARE	GLU A:37 , GLN C:16 , GLU C:19 , HOH C:507 , HOH C:508	BINDING SITE FOR RESIDUE MN C 505
12	BC3	SOFTWARE	LEU A:9 , GLU A:10 , ALA A:13 , GLU A:36 , MN A:401 , LEU B:9 , GLU B:10 , ALA B:13 , GLU B:36 , MN B:402	BINDING SITE FOR RESIDUE DMS B 301
13	BC4	SOFTWARE	LEU C:9 , GLU C:10 , ALA C:13 , GLU C:36 , MN C:403 , GLU D:10 , ALA D:13 , GLU D:36 , MN D:404	BINDING SITE FOR RESIDUE DMS C 302
14	BC5	SOFTWARE	GLU E:10 , GLU E:36 , MN E:405 , LEU F:9 , GLU F:10 , ALA F:13 , GLU F:36 , MN F:406	BINDING SITE FOR RESIDUE DMS F 303

(no "SS Bond" information available for 1JM0)

(no "Cis Peptide Bond" information available for 1JM0)

(no "SAP(SNP)/Variant" information available for 1JM0)

(no "PROSITE Motif" information available for 1JM0)

(no "Exon" information available for 1JM0)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:50
                                                                                 
               SCOP domains d1jm0a_ A: Artificial diiron protein               SCOP domains
               CATH domains -1jm0A00 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
                  1jm0 A  0 xDYLRELLKLELQAIKQYREALEYVKLPVLAKILEDEEKHIEWLETILGx 49
                            |        9        19        29        39        49
                            |                                               49-NH2
                            0-ACE

Chain B from PDB  Type:PROTEIN  Length:50
                                                                                 
               SCOP domains d1jm0b_ B: Artificial diiron protein               SCOP domains
               CATH domains -1jm0B00 B:1-48 Immunoglobulin FC, subunit C     - CATH domains
               Pfam domains -------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------- Transcript
                  1jm0 B  0 xDYLRELLKLELQAIKQYREALEYVKLPVLAKILEDEEKHIEWLETILGx 49
                            |        9        19        29        39        49
                            |                                               49-NH2
                            0-ACE

Chain C from PDB  Type:PROTEIN  Length:50
                                                                                 
               SCOP domains d1jm0c_ C: Artificial diiron protein               SCOP domains
               CATH domains -1jm0C00 C:1-48 Immunoglobulin FC, subunit C     - CATH domains
               Pfam domains -------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------- Transcript
                  1jm0 C  0 xDYLRELLKLELQAIKQYREALEYVKLPVLAKILEDEEKHIEWLETILGx 49
                            |        9        19        29        39        49
                            |                                               49-NH2
                            0-ACE

Chain D from PDB  Type:PROTEIN  Length:50
                                                                                 
               SCOP domains d1jm0d_ D: Artificial diiron protein               SCOP domains
               CATH domains -1jm0D00 D:1-48 Immunoglobulin FC, subunit C     - CATH domains
               Pfam domains -------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------- Transcript
                  1jm0 D  0 xDYLRELLKLELQAIKQYREALEYVKLPVLAKILEDEEKHIEWLETILGx 49
                            |        9        19        29        39        49
                            |                                               49-NH2
                            0-ACE

Chain E from PDB  Type:PROTEIN  Length:50
                                                                                 
               SCOP domains d1jm0e_ E: Artificial diiron protein               SCOP domains
               CATH domains -1jm0E00 E:1-48 Immunoglobulin FC, subunit C     - CATH domains
               Pfam domains -------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------- Transcript
                  1jm0 E  0 xDYLRELLKLELQAIKQYREALEYVKLPVLAKILEDEEKHIEWLETILGx 49
                            |        9        19        29        39        49
                            |                                               49-NH2
                            0-ACE

Chain F from PDB  Type:PROTEIN  Length:50
                                                                                 
               SCOP domains d1jm0f_ F: Artificial diiron protein               SCOP domains
               CATH domains -1jm0F00 F:1-48 Immunoglobulin FC, subunit C     - CATH domains
               Pfam domains -------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------- Transcript
                  1jm0 F  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	d1jm0a_	A:
1b	d1jm0b_	B:
1c	d1jm0c_	C:
1d	d1jm0d_	D:
1e	d1jm0e_	E:
1f	d1jm0f_	F:

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	1jm0A00	A:1-48
1b	1jm0B00	B:1-48
1c	1jm0C00	C:1-48
1d	1jm0D00	D:1-48
1e	1jm0E00	E:1-48
1f	1jm0F00	F:1-48

(no "Pfam Domain" information available for 1JM0)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 1JM0)

Asymmetric Unit
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1ec5	1EC5 IS THE ZINC DERIVATIVE WITH ALA13 RESIDUE MUTATED TO LEU
1jmb	1JMB IS A DIFFERENT CRYSTALLINE FORM (S.G. C 2 2 21) OF THE SAME STRUCTURE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 26)

Sites (14, 14)

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 (1, 6)

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