1V8C - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF MOAD RELATED PROTEIN FROM THERMUS THERMOPHILUS HB8

Authors :   H. Mizutani, N. Kunishima, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   05 Jan 04 (Deposition) - 20 Jan 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   Moad Related Protein, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Mizutani, N. Kunishima
Crystal Structure Of Moad Related Protein From Thermus Thermophilus Hb8
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - MOAD RELATED PROTEIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	274

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (1x)	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:67 , LEU A:68 , HOH A:1038 , TRP C:108 , ARG C:158	BINDING SITE FOR RESIDUE CL A 1002
2	AC2	SOFTWARE	ARG B:158 , GLY D:67 , LEU D:68 , HOH D:221	BINDING SITE FOR RESIDUE CL B 1003
3	AC3	SOFTWARE	ARG A:63 , HOH A:1003 , ARG C:154 , TRP C:155	BINDING SITE FOR RESIDUE EDO A 1001

(no "SS Bond" information available for 1V8C)

(no "Cis Peptide Bond" information available for 1V8C)

(no "SAP(SNP)/Variant" information available for 1V8C)

(no "PROSITE Motif" information available for 1V8C)

(no "Exon" information available for 1V8C)

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:165
 aligned with P83826_THETH | P83826 from UniProtKB/TrEMBL  Length:168

    Alignment length:165
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160     
         P83826_THETH     1 PKVNLYATFRDLTGKSQLELPGATVGEVLENLVRAYPALKEELFEGEGLAERVSVFLEGRDVRYLQGLSTPLSPGATLDLFPPVAGGGFERTFGAFPPWLLERYLEEWGGTREGEGVYRLPGAVVRFREVEPLKVGSLSIPQLRVEVEGEEAERWFERIAFAASR 165
               SCOP domains d1v8ca1 A:1-87 MoaD-related protein, N-terminal domain                                 d1v8ca2 A:88-165 MoaD-related protein, C-terminal domain                       SCOP domains
               CATH domains 1v8cA01 A:1-85  [code=3.10.20.30, no name defined]                                   1v8cA02 A:86-165 moad related protein, domain 2                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.hhhhhhhh..eee....hhhhhhhhhhhhh..hhhhhee..ee....eeee..ee.hhhhhhhh......eeeee.....eeeeeeee..hhhhhhhhhhhh..eeee..eeee..eeeeeeeeeeeee..eeeeeeeeeeee.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v8c A   1 PKVNLYATFRDLTGKSQLELPGATVGEVLENLVRAYPALKEELFEGEGLAERVSVFLEGRDVRYLQGLSTPLSPGATLDLFPPVAGGGFERTFGAFPPWLLERYLEEWGGTREGEGVYRLPGAVVRFREVEPLKVGSLSIPQLRVEVEGEEAERWFERIAFAASR 165
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain B from PDB  Type:PROTEIN  Length:160
 aligned with P83826_THETH | P83826 from UniProtKB/TrEMBL  Length:168

    Alignment length:164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    
         P83826_THETH     1 PKVNLYATFRDLTGKSQLELPGATVGEVLENLVRAYPALKEELFEGEGLAERVSVFLEGRDVRYLQGLSTPLSPGATLDLFPPVAGGGFERTFGAFPPWLLERYLEEWGGTREGEGVYRLPGAVVRFREVEPLKVGSLSIPQLRVEVEGEEAERWFERIAFAAS 164
               SCOP domains d1v8cb1 B:1-83 MoaD-related protein, N-terminal domain                             ----d1v8cb2 B:88-164 MoaD-related protein, C-terminal domain                      SCOP domains
               CATH domains 1v8cB01 B:1-83  [code=3.10.20.30, no name defined]                                 ----1v8cB02 B:88-164 moad related protein, domain 2                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.hhhhhhhh..eee....hhhhhhhhhhhhh..hhhhhee..ee....eeee..ee.hhhhhhhh......eeeee..----.eeeeee..hhhhhhhhhhhh..eeee..eeee..eeeeeeeeeeeee..eeeeeeeeeee..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v8c B   1 PKVNLYATFRDLTGKSQLELPGATVGEVLENLVRAYPALKEELFEGEGLAERVSVFLEGRDVRYLQGLSTPLSPGATLDLFPP----GFERTFGAFPPWLLERYLEEWGGTREGEGVYRLPGAVVRFREVEPLKVGSLSIPQLRVEVEGEEAERWFERIAFAAS 164
                                    10        20        30        40        50        60        70        80  |    |90       100       110       120       130       140       150       160    
                                                                                                             83   88

Chain C from PDB  Type:PROTEIN  Length:165
 aligned with P83826_THETH | P83826 from UniProtKB/TrEMBL  Length:168

    Alignment length:165
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160     
         P83826_THETH     1 PKVNLYATFRDLTGKSQLELPGATVGEVLENLVRAYPALKEELFEGEGLAERVSVFLEGRDVRYLQGLSTPLSPGATLDLFPPVAGGGFERTFGAFPPWLLERYLEEWGGTREGEGVYRLPGAVVRFREVEPLKVGSLSIPQLRVEVEGEEAERWFERIAFAASR 165
               SCOP domains d1v8cc1 C:1-87 MoaD-related protein, N-terminal domain                                 d1v8cc2 C:88-165 MoaD-related protein, C-terminal domain                       SCOP domains
               CATH domains 1v8cC01 C:1-85  [code=3.10.20.30, no name defined]                                   1v8cC02 C:86-165 moad related protein, domain 2                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.hhhhhhhh..eee....hhhhhhhhhhhhh..hhhhhee..ee....eeee..ee.hhhhhhhh......eeeee......eeeeeee..hhhhhhhhhhhh..eeee..eeee..eeeeeeeeeeeee..eeeeeeeeeee..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v8c C   1 PKVNLYATFRDLTGKSQLELPGATVGEVLENLVRAYPALKEELFEGEGLAERVSVFLEGRDVRYLQGLSTPLSPGATLDLFPPVAGGGFERTFGAFPPWLLERYLEEWGGTREGEGVYRLPGAVVRFREVEPLKVGSLSIPQLRVEVEGEEAERWFERIAFAASR 165
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain D from PDB  Type:PROTEIN  Length:165
 aligned with P83826_THETH | P83826 from UniProtKB/TrEMBL  Length:168

    Alignment length:165
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160     
         P83826_THETH     1 PKVNLYATFRDLTGKSQLELPGATVGEVLENLVRAYPALKEELFEGEGLAERVSVFLEGRDVRYLQGLSTPLSPGATLDLFPPVAGGGFERTFGAFPPWLLERYLEEWGGTREGEGVYRLPGAVVRFREVEPLKVGSLSIPQLRVEVEGEEAERWFERIAFAASR 165
               SCOP domains d1v8cd1 D:1-87 MoaD-related protein, N-terminal domain                                 d1v8cd2 D:88-165 MoaD-related protein, C-terminal domain                       SCOP domains
               CATH domains 1v8cD01 D:1-85  [code=3.10.20.30, no name defined]                                   1v8cD02 D:86-165 moad related protein, domain 2                                  CATH domains
           Pfam domains (1) --ThiS-1v8cD01 D:3-87                                                                  DUF1952-1v8cD05 D:88-165                                                       Pfam domains (1)
           Pfam domains (2) --ThiS-1v8cD02 D:3-87                                                                  DUF1952-1v8cD06 D:88-165                                                       Pfam domains (2)
           Pfam domains (3) --ThiS-1v8cD03 D:3-87                                                                  DUF1952-1v8cD07 D:88-165                                                       Pfam domains (3)
           Pfam domains (4) --ThiS-1v8cD04 D:3-87                                                                  DUF1952-1v8cD08 D:88-165                                                       Pfam domains (4)
         Sec.struct. author .eeee.hhhhhhhh..eee....hhhhhhhhhhhhh..hhhhhee..ee....eeee..ee.hhhhhhhh......eeeee......eeeeeee..hhhhhhhhhhhh..eeee..eeee..eeeeeeeeeeeee..eeeeeeeeeee..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v8c D   1 PKVNLYATFRDLTGKSQLELPGATVGEVLENLVRAYPALKEELFEGEGLAERVSVFLEGRDVRYLQGLSTPLSPGATLDLFPPVAGGGFERTFGAFPPWLLERYLEEWGGTREGEGVYRLPGAVVRFREVEPLKVGSLSIPQLRVEVEGEEAERWFERIAFAASR 165
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

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: Alpha and beta proteins (a+b) (23004)

Fold: beta-Grasp (ubiquitin-like) (1032)

Superfamily: MoaD/ThiS (25)

Family: MoaD (9)

Protein domain: MoaD-related protein, N-terminal domain (1)

Thermus thermophilus [TaxId: 274] (1)

1a	d1v8ca1	A:1-87
1b	d1v8cb1	B:1-83
1c	d1v8cc1	C:1-87
1d	d1v8cd1	D:1-87

Fold: TBP-like (289)

Superfamily: MoaD-related protein, C-terminal domain (1)

Family: MoaD-related protein, C-terminal domain (1)

Protein domain: MoaD-related protein, C-terminal domain (1)

Thermus thermophilus [TaxId: 274] (1)

2a	d1v8ca2	A:88-165
2b	d1v8cb2	B:88-164
2c	d1v8cc2	C:88-165
2d	d1v8cd2	D:88-165

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Ribosomal Protein S8; Chain: A, domain 1 (139)

Homologous Superfamily: moad related protein, domain 2 (1)

Thermus thermophilus. Organism_taxid: 274. (1)

1a	1v8cA02	A:86-165
1b	1v8cC02	C:86-165
1c	1v8cD02	D:86-165
1d	1v8cB02	B:88-164

Architecture: Roll (3276)

Topology: Ubiquitin-like (UB roll) (674)

Homologous Superfamily: [code=3.10.20.30, no name defined] (153)

Thermus thermophilus. Organism_taxid: 274. (1)

2a	1v8cA01	A:1-85
2b	1v8cC01	C:1-85
2c	1v8cD01	D:1-85
2d	1v8cB01	B:1-83

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ubiquitin (279)

Family: ThiS (18)

Thermus thermophilus (1)

1a	ThiS-1v8cD01	D:3-87
1b	ThiS-1v8cD02	D:3-87
1c	ThiS-1v8cD03	D:3-87
1d	ThiS-1v8cD04	D:3-87

Clan: no clan defined [family: DUF1952] (1)

Family: DUF1952 (1)

Thermus thermophilus (1)

2a	DUF1952-1v8cD05	D:88-165
2b	DUF1952-1v8cD06	D:88-165
2c	DUF1952-1v8cD07	D:88-165
2d	DUF1952-1v8cD08	D:88-165

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (P83826_THETH | P83826)

molecular function
	GO:0004795		threonine synthase activity		Catalysis of the reaction: O-phospho-L-homoserine + H2O = L-threonine + phosphate.

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Description

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Ligands, Modified Residues, Ions (2, 3)

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