3FOP - JenaLib

Title :   A TRIANGULAR CYTOCHROME B562 SUPERSTRUCTURE MEDIATED BY NI COORDINATION - HEXAGONAL FORM

Authors :   F. A. Tezcan, R. J. Radford

Date :   30 Dec 08 (Deposition) - 14 Jul 09 (Release) - 14 Jul 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

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

Keywords :   Four Helix Bundle, Electron Transport, Heme, Iron, Metal- Binding, Periplasm, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. J. Radford, F. A. Tezcan
A Superprotein Triangle Driven By Nickel(Ii) Coordination: Exploiting Non-Natural Metal Ligands In Protein Self-Assembly.
J. Am. Chem. Soc. V. 131 9136 2009
PubMed-ID: 19527025 | Reference-DOI: 10.1021/JA9000695
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Asymmetric Unit (3, 8)

No.	Name	Count	Type	Full Name
1	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	NI	4	Ligand/Ion	NICKEL (II) ION
3	PXX	2	Ligand/Ion	N-1,10-PHENANTHROLIN-5-YLACETAMIDE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	NI	-1	Ligand/Ion	NICKEL (II) ION
3	PXX	1	Ligand/Ion	N-1,10-PHENANTHROLIN-5-YLACETAMIDE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	NI	-1	Ligand/Ion	NICKEL (II) ION
3	PXX	1	Ligand/Ion	N-1,10-PHENANTHROLIN-5-YLACETAMIDE

Biological Unit 3 (2, 4)

No.	Name	Count	Type	Full Name
1	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	NI	-1	Ligand/Ion	NICKEL (II) ION
3	PXX	2	Ligand/Ion	N-1,10-PHENANTHROLIN-5-YLACETAMIDE

Sites (8, 8)

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:4 , MET A:7 , ASN A:11 , PRO A:46 , PHE A:61 , PHE A:65 , CYS A:98 , CYS A:101 , HIS A:102 , TYR A:105 , ARG A:106 , HOH A:112	BINDING SITE FOR RESIDUE HEM A 150
2	AC2	SOFTWARE	GLN A:41 , LYS A:42 , ALA A:43 , PRO A:53 , MET A:58 , CYS A:59 , ALA A:62 , ASP A:73 , ASP A:74 , HIS A:77 , NI A:109 , HOH A:115	BINDING SITE FOR RESIDUE PXX A 151
3	AC3	SOFTWARE	HIS A:77 , HOH A:115 , HOH A:116 , PXX A:151	BINDING SITE FOR RESIDUE NI A 109
4	AC4	SOFTWARE	ALA A:1 , ASP A:39 , HOH A:111	BINDING SITE FOR RESIDUE NI A 110
5	AC5	SOFTWARE	GLU B:4 , MET B:7 , GLU B:8 , ASN B:11 , PRO B:46 , PHE B:61 , PHE B:65 , CYS B:98 , CYS B:101 , HIS B:102 , TYR B:105 , ARG B:106	BINDING SITE FOR RESIDUE HEM B 150
6	AC6	SOFTWARE	GLN B:41 , LYS B:42 , ALA B:43 , PRO B:53 , MET B:58 , CYS B:59 , ALA B:62 , ASP B:73 , ASP B:74 , HIS B:77 , NI B:109	BINDING SITE FOR RESIDUE PXX B 151
7	AC7	SOFTWARE	HIS B:77 , HOH B:116 , PXX B:151	BINDING SITE FOR RESIDUE NI B 109
8	AC8	SOFTWARE	ALA B:1 , ASP B:39	BINDING SITE FOR RESIDUE NI B 110

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

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:106
 aligned with C562_ECOLX | P0ABE7 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:106
                                    32        42        52        62        72        82        92       102       112       122      
           C562_ECOLX    23 ADLEDNMETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYHQKYR 128
               SCOP domains d3fopa_ A: automated matches                                                                               SCOP domains
               CATH domains 3fopA00 A:1-106  [code=1.20.120.10, no name defined]                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 3fop A   1 ADLEDNMETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMCDFAAGFHILVGQIDDALHLANEGKVKEAQAAAEQLKTTCNACHQKYR 106
                                    10        20        30        40        50        60        70        80        90       100

Chain B from PDB  Type:PROTEIN  Length:106
 aligned with C562_ECOLX | P0ABE7 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:106
                                    32        42        52        62        72        82        92       102       112       122      
           C562_ECOLX    23 ADLEDNMETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYHQKYR 128
               SCOP domains d3fopb_ B: automated matches                                                                               SCOP domains
               CATH domains 3fopB00 B:1-106  [code=1.20.120.10, no name defined]                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 3fop B   1 ADLEDNMETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMCDFAAGFHILVGQIDDALHLANEGKVKEAQAAAEQLKTTCNACHQKYR 106
                                    10        20        30        40        50        60        70        80        90       100

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	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 '\|'

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

Asymmetric Unit(hide GO term definitions)

Chain A,B (C562_ECOLX | P0ABE7)

molecular function
	GO:0009055	electron carrier activity	Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	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.
biological process
	GO:0022900	electron transport chain	A process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
	GO:0042597	periplasmic space	The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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