1C5E - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   BACTERIOPHAGE LAMBDA HEAD PROTEIN D

Authors :   F. Yang, P. Forrer, Z. Dauter, A. Pluckthun, A. Wlodawer

Date :   18 Nov 99 (Deposition) - 08 Mar 00 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.10

Chains :   Asym./Biol. Unit : A,B,C

Keywords :   Bacteriophage Lambda, Head Protein D, Protein Crystal Structure, Virus Assembly, Phage Display, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Yang, P. Forrer, Z. Dauter, J. F. Conway, N. Cheng, M. E. Cerritelli, A. C. Steven, A. Pluckthun, A. Wlodawer
Novel Fold And Capsid-Binding Properties Of The Lambda-Phag Display Platform Protein Gpd.
Nat. Struct. Biol. V. 7 230 2000
PubMed-ID: 10700283 | Reference-DOI: 10.1038/73347

Molecule 1 - HEAD DECORATION PROTEIN
	Chains	:	A, B, C
	Engineered	:	YES
	Organism Scientific	:	ENTEROBACTERIA PHAGE LAMBDA
	Organism Taxid	:	10710
	Synonym	:	GPD, MAJOR CAPSID PROTEIN D

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL A:63 , ALA A:64 , ALA A:65 , THR A:71 , LEU A:72 , THR A:73 , HOH A:904 , HOH A:908 , HOH B:624	BINDING SITE FOR RESIDUE GOL A 599
2	AC2	SOFTWARE	HOH A:638 , LEU C:61 , VAL C:63 , ALA C:65 , THR C:71 , LEU C:72 , THR C:73 , HOH C:906 , HOH C:909	BINDING SITE FOR RESIDUE GOL C 600

(no "SS Bond" information available for 1C5E)

(no "Cis Peptide Bond" information available for 1C5E)

(no "SAP(SNP)/Variant" information available for 1C5E)

(no "PROSITE Motif" information available for 1C5E)

(no "Exon" information available for 1C5E)

Asymmetric/Biological 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:95
 aligned with DECO_LAMBD | P03712 from UniProtKB/Swiss-Prot  Length:110

    Alignment length:95
                                    25        35        45        55        65        75        85        95       105     
           DECO_LAMBD    16 SDPAHTATAPGGLSAKAPAMTPLMLDTSSRKLVAWDGTTDGAAVGILAVAADQTSTTLTFYKSGTFRYEDVLWPEAASDETKKRTAFAGTAISIV 110
               SCOP domains d1c5ea_ A: Head decoration protein D (gpD, major capsid protein D)                              SCOP domains
               CATH domains 1c5eA00 A:15-109  [code=2.40.300.10, no name defined]                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee...........eeee......eee........eeee..........eeeee.eeeee............hhhhh......eeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 1c5e A  15 SDPAHTATAPGGLSAKAPAMTPLMLDTSSRKLVAWDGTTDGAAVGILAVAADQTSTTLTFYKSGTFRYEDVLWPEAASDETKKRTAFAGTAISIV 109
                                    24        34        44        54        64        74        84        94       104

Chain B from PDB  Type:PROTEIN  Length:95
 aligned with DECO_LAMBD | P03712 from UniProtKB/Swiss-Prot  Length:110

    Alignment length:95
                                    25        35        45        55        65        75        85        95       105     
           DECO_LAMBD    16 SDPAHTATAPGGLSAKAPAMTPLMLDTSSRKLVAWDGTTDGAAVGILAVAADQTSTTLTFYKSGTFRYEDVLWPEAASDETKKRTAFAGTAISIV 110
               SCOP domains d1c5eb_ B: Head decoration protein D (gpD, major capsid protein D)                              SCOP domains
               CATH domains 1c5eB00 B:15-109  [code=2.40.300.10, no name defined]                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee...........eeee......eee........eeee..........eeeee.eeeee............hhhhh......eeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 1c5e B  15 SDPAHTATAPGGLSAKAPAMTPLMLDTSSRKLVAWDGTTDGAAVGILAVAADQTSTTLTFYKSGTFRYEDVLWPEAASDETKKRTAFAGTAISIV 109
                                    24        34        44        54        64        74        84        94       104

Chain C from PDB  Type:PROTEIN  Length:95
 aligned with DECO_LAMBD | P03712 from UniProtKB/Swiss-Prot  Length:110

    Alignment length:95
                                    25        35        45        55        65        75        85        95       105     
           DECO_LAMBD    16 SDPAHTATAPGGLSAKAPAMTPLMLDTSSRKLVAWDGTTDGAAVGILAVAADQTSTTLTFYKSGTFRYEDVLWPEAASDETKKRTAFAGTAISIV 110
               SCOP domains d1c5ec_ C: Head decoration protein D (gpD, major capsid protein D)                              SCOP domains
               CATH domains 1c5eC00 C:15-109  [code=2.40.300.10, no name defined]                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee...........eeee......eee........eeee..........eeeee.eeeee............hhhhh......eeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 1c5e C  15 SDPAHTATAPGGLSAKAPAMTPLMLDTSSRKLVAWDGTTDGAAVGILAVAADQTSTTLTFYKSGTFRYEDVLWPEAASDETKKRTAFAGTAISIV 109
                                    24        34        44        54        64        74        84        94       104

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: beta-clip (280)

Superfamily: Head decoration protein D (gpD, major capsid protein D) (6)

Family: Head decoration protein D (gpD, major capsid protein D) (6)

Protein domain: Head decoration protein D (gpD, major capsid protein D) (5)

Bacteriophage lambda [TaxId: 10710] (2)

1a	d1c5ea_	A:
1b	d1c5eb_	B:
1c	d1c5ec_	C:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Virus Head Decoration Protein; Chain: A, (6)

Homologous Superfamily: [code=2.40.300.10, no name defined] (6)

Enterobacteria phage lambda. Organism_taxid: 10710 (1)

1a	1c5eA00	A:15-109
1b	1c5eB00	B:15-109
1c	1c5eC00	C:15-109

(no "Pfam Domain" information available for 1C5E)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C (DECO_LAMBD | P03712)

biological process
	GO:0019076	viral release from host cell	The dissemination of mature viral particles from the host cell, e.g. by cell lysis or the budding of virus particles from the cell membrane.
cellular component
	GO:0030430	host cell cytoplasm	The cytoplasm of a host cell.
	GO:0019028	viral capsid	The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
	GO:0098021	viral capsid, decoration	Component of the virus capsid (head), located on the outer head surface. Involved in the stabilization of the head structure and usually non-essential.
	GO:0019012	virion	The complete fully infectious extracellular virus particle.

Asymmetric/Biological Unit
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(no "Related Entries Specified in the PDB File" available for 1C5E)

Description

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Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

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