2PVE - JenaLib

Title :   NMR AND X-RAY ANALYSIS OF STRUCTURAL ADDITIVITY IN METAL BINDING SITE-SWAPPED HYBRIDS OF RUBREDOXIN

Authors :   D. M. Lemaster, J. S. Anderson, L. Wang, Y. Guo, H. Li, G. Hernandez

Date :   09 May 07 (Deposition) - 18 Dec 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   0.79

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

Keywords :   Rubredoxin, Ultrahigh Resolution, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. M. Lemaster, J. S. Anderson, L. Wang, Y. Guo, H. Li, G. Hernandez
Nmr And X-Ray Analysis Of Structural Additivity In Metal Binding Site-Swapped Hybrids Of Rubredoxin.
Bmc Struct. Biol. V. 7 81 2007
PubMed-ID: 18053245 | Reference-DOI: 10.1186/1472-6807-7-81
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (7, 7)

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:6 , CYS A:9 , CYS A:39 , CYS A:42	BINDING SITE FOR RESIDUE ZN A 301
2	AC2	SOFTWARE	CYS B:106 , CYS B:109 , CYS B:139 , CYS B:142	BINDING SITE FOR RESIDUE ZN B 302
3	AC3	SOFTWARE	CYS C:206 , CYS C:209 , CYS C:239 , CYS C:242	BINDING SITE FOR RESIDUE ZN C 303
4	AC4	SOFTWARE	PRO B:120 , ASP C:235 , SER C:247 , HOH C:1139 , HOH C:1173 , HOH C:1174	BINDING SITE FOR RESIDUE ACT C 401
5	AC5	SOFTWARE	PRO A:45 , LYS A:46 , SER A:47	BINDING SITE FOR RESIDUE ACT A 501
6	AC6	SOFTWARE	MET A:1 , LYS A:2 , TYR A:4 , ASP A:29 , LYS A:31 , HOH A:1248	BINDING SITE FOR RESIDUE ACT A 601
7	AC7	SOFTWARE	ASP B:135 , PRO B:145 , LYS B:146 , SER B:147 , HOH B:1067 , HOH B:1143 , HOH B:1225	BINDING SITE FOR RESIDUE EDO B 701

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 6)

Asymmetric Unit (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RUBREDOXIN_LIKE	PS50903	Rubredoxin-like domain profile.	RUBR_CLOPA	1-52	3	A:1-52 B:101-152 C:201-252
2	RUBREDOXIN	PS00202	Rubredoxin signature.	RUBR_CLOPA	33-43	3	A:33-43 B:133-143 C:233-243

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RUBREDOXIN_LIKE	PS50903	Rubredoxin-like domain profile.	RUBR_CLOPA	1-52	1	A:1-52 - -
2	RUBREDOXIN	PS00202	Rubredoxin signature.	RUBR_CLOPA	33-43	1	A:33-43 - -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RUBREDOXIN_LIKE	PS50903	Rubredoxin-like domain profile.	RUBR_CLOPA	1-52	1	- B:101-152 -
2	RUBREDOXIN	PS00202	Rubredoxin signature.	RUBR_CLOPA	33-43	1	- B:133-143 -

Biological Unit 3 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RUBREDOXIN_LIKE	PS50903	Rubredoxin-like domain profile.	RUBR_CLOPA	1-52	1	- - C:201-252
2	RUBREDOXIN	PS00202	Rubredoxin signature.	RUBR_CLOPA	33-43	1	- - C:233-243

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:52
 aligned with RUBR_CLOPA | P00268 from UniProtKB/Swiss-Prot  Length:54

    Alignment length:52
                                    10        20        30        40        50  
           RUBR_CLOPA     1 MKKYTCTVCGYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPLCGVGKDQFEEV  52
               SCOP domains d2pvea_ A: automated matches                         SCOP domains
               CATH domains 2pveA00 A:1-52  [code=2.20.28.10, no name defined]   CATH domains
               Pfam domains ---------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.....ee.....hhhhh.....hhhhh...........hhh.eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------- SAPs(SNPs)
                PROSITE (1) RUBREDOXIN_LIKE  PDB: A:1-52 UniProt: 1-52           PROSITE (1)
                PROSITE (2) --------------------------------RUBREDOXIN --------- PROSITE (2)
                 Transcript ---------------------------------------------------- Transcript
                 2pve A   1 MKKYTCKICGYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPICGAPKSEFEEV  52
                                    10        20        30        40        50

Chain B from PDB  Type:PROTEIN  Length:52
 aligned with RUBR_CLOPA | P00268 from UniProtKB/Swiss-Prot  Length:54

    Alignment length:52
                                    10        20        30        40        50  
           RUBR_CLOPA     1 MKKYTCTVCGYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPLCGVGKDQFEEV  52
               SCOP domains d2pveb_ B: automated matches                         SCOP domains
               CATH domains 2pveB00 B:101-152                                    CATH domains
               Pfam domains ---------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.....ee.....hhhhh.....hhhhh...........hhh.eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------- SAPs(SNPs)
                PROSITE (1) RUBREDOXIN_LIKE  PDB: B:101-152 UniProt: 1-52        PROSITE (1)
                PROSITE (2) --------------------------------RUBREDOXIN --------- PROSITE (2)
                 Transcript ---------------------------------------------------- Transcript
                 2pve B 101 MKKYTCKICGYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPICGAPKSEFEEV 152
                                   110       120       130       140       150

Chain C from PDB  Type:PROTEIN  Length:52
 aligned with RUBR_CLOPA | P00268 from UniProtKB/Swiss-Prot  Length:54

    Alignment length:52
                                    10        20        30        40        50  
           RUBR_CLOPA     1 MKKYTCTVCGYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPLCGVGKDQFEEV  52
               SCOP domains d2pvec_ C: automated matches                         SCOP domains
               CATH domains 2pveC00 C:201-252                                    CATH domains
           Pfam domains (1) --Rubredoxin-2pveC01 C:203-249                   --- Pfam domains (1)
           Pfam domains (2) --Rubredoxin-2pveC02 C:203-249                   --- Pfam domains (2)
           Pfam domains (3) --Rubredoxin-2pveC03 C:203-249                   --- Pfam domains (3)
         Sec.struct. author ...eee.....ee.....hhhhh.....hhhhh...........hhh.eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------- SAPs(SNPs)
                PROSITE (1) RUBREDOXIN_LIKE  PDB: C:201-252 UniProt: 1-52        PROSITE (1)
                PROSITE (2) --------------------------------RUBREDOXIN --------- PROSITE (2)
                 Transcript ---------------------------------------------------- Transcript
                 2pve C 201 MKKYTCKICGYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPICGAPKSEFEEV 252
                                   210       220       230       240       250

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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, 3)

CATH Domains (1, 3)

Pfam Domains (1, 3)

Gene Ontology (4, 4)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (RUBR_CLOPA | P00268)

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: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: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.

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