4F46 - JenaLib

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Title :   CRYSTAL STRUCTURE OF WILD TYPE HUMAN CD38 IN COMPLEX WITH NAADP AND ADPRP

Authors :   H. Zhang, H. C. Lee, Q. Hao

Date :   10 May 12 (Deposition) - 03 Apr 13 (Release) - 03 Apr 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.69

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

Keywords :   Cd38, Adp-Ribosyl Cyclase, Naadp, Calcium Signaling, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Zhang, R. Graeff, H. C. Lee, Q. Hao
Crystal Structures Of Human Cd38 In Complex With Naadp And Adprp
Messenger V. 2 44 2013
PubMed: search

Molecule 1 - ADP-RIBOSYL CYCLASE 1
	Chains	:	A, B
	EC Number	:	3.2.2.5
	Engineered	:	YES
	Expression System	:	PICHIA PASTORIS
	Expression System Plasmid	:	PPICZALPHA
	Expression System Strain	:	X33
	Expression System Taxid	:	4922
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 46-300
	Gene	:	CD38
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CYCLIC ADP-RIBOSE HYDROLASE 1, CADPR HYDROLASE 1, T10

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 2)

No.	Name	Count	Type	Full Name
1	DN4	1	Ligand/Ion	[[(2R,3R,4R,5R)-5-(6-AMINOPURIN-9-YL)-3-OXIDANYL-4-PHOSPHONOOXY-OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL][(2R,3S,4R,5R)-5-(3-CARBOXYPYRIDIN-1-IUM-1-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHYL PHOSPHATE
2	DVN	1	Ligand/Ion	[[(2R,3R,4R,5R)-5-(6-AMINOPURIN-9-YL)-3-OXIDANYL-4-PHOSPHONOOXY-OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL][(2R,3S,4R,5S)-3,4,5-TRIS(OXIDANYL)OXOLAN-2-YL]METHYLHYDROGEN PHOSPHATE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	DN4	-1	Ligand/Ion	[[(2R,3R,4R,5R)-5-(6-AMINOPURIN-9-YL)-3-OXIDANYL-4-PHOSPHONOOXY-OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL][(2R,3S,4R,5R)-5-(3-CARBOXYPYRIDIN-1-IUM-1-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHYL PHOSPHATE
2	DVN	1	Ligand/Ion	[[(2R,3R,4R,5R)-5-(6-AMINOPURIN-9-YL)-3-OXIDANYL-4-PHOSPHONOOXY-OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL][(2R,3S,4R,5S)-3,4,5-TRIS(OXIDANYL)OXOLAN-2-YL]METHYLHYDROGEN PHOSPHATE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	DN4	1	Ligand/Ion	[[(2R,3R,4R,5R)-5-(6-AMINOPURIN-9-YL)-3-OXIDANYL-4-PHOSPHONOOXY-OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL][(2R,3S,4R,5R)-5-(3-CARBOXYPYRIDIN-1-IUM-1-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHYL PHOSPHATE
2	DVN	-1	Ligand/Ion	[[(2R,3R,4R,5R)-5-(6-AMINOPURIN-9-YL)-3-OXIDANYL-4-PHOSPHONOOXY-OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL][(2R,3S,4R,5S)-3,4,5-TRIS(OXIDANYL)OXOLAN-2-YL]METHYLHYDROGEN PHOSPHATE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:125 , SER A:126 , ARG A:127 , LYS A:129 , LEU A:145 , GLU A:146 , VAL A:185 , TRP A:189 , SER A:193 , SER A:220 , THR A:221 , PHE A:222 , GLU A:226 , HOH A:506 , HOH A:550 , HOH A:614 , HOH A:624 , HOH A:682 , HOH A:699 , HOH A:700	BINDING SITE FOR RESIDUE DVN A 401
2	AC2	SOFTWARE	LEU B:124 , TRP B:125 , SER B:126 , ARG B:127 , LYS B:129 , LEU B:145 , GLU B:146 , ASP B:155 , TRP B:189 , SER B:193 , SER B:220 , THR B:221 , PHE B:222 , GLU B:226 , HOH B:504 , HOH B:670	BINDING SITE FOR RESIDUE DN4 B 401

Asymmetric Unit

No.	Residues
1	A:67	-	A:82
2	A:99	-	A:180
3	A:119	-	A:201
4	A:160	-	A:173
5	A:254	-	A:275
6	B:67	-	B:82
7	B:99	-	B:180
8	B:119	-	B:201
9	B:160	-	B:173
10	B:254	-	B:275
11	B:287	-	B:296

(no "Cis Peptide Bond" information available for 4F46)

(no "SAP(SNP)/Variant" information available for 4F46)

(no "PROSITE Motif" information available for 4F46)

(no "Exon" information available for 4F46)

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
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Chain A from PDB  Type:PROTEIN  Length:248
                                                                                                                                                                                                                                                                                        
               SCOP domains d4f46a_ A: ADP ribosyl cyclase                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........ee....hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.......hhhhhhhhhhhh.........eeee.hhhhhhhhhhhh....hhhhhhhhhhhh................ee.........hhhhhhhhhhhhhhhhhh.eeeeeeee..........hhhhhhhhhhh....eeeeeeeee........hhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f46 A  44 EFWRQTWSGPGTTKRFPETVLARCVKYTEIHPEMRHVDCQSVWDAFKGAFISKHPCDITEEDYQPLMKLGTQTVPCNKILLWSRIKDLAHQFTQVQRDMFTLEDTLLGYLADDLTWCGEFDTSKINYQSCPDWRKDCSNNPVSVFWKTVSRRFAEAACDVVHVMLDGSRSKIFDKDSTFGSVEVHNLQPEKVQTLEAWVIHGGREDSRDLCQDPTIKELESIISKRNIQFSCKNIYRPDKFLQCVKNP 291
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283

Chain B from PDB  Type:PROTEIN  Length:252
                                                                                                                                                                                                                                                                                            
               SCOP domains d4f46b_ B: ADP ribosyl cyclase                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......ee....hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.......hhhhhhhhhhhh.........eeee.hhhhhhhhhhhh....hhhhhhhhhhhh................ee.........hhhhhhhhhhhhhhhhhh.eeeeeeee..........hhhhhhhhhhh....eeeeeeeee........hhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4f46 B  45 FWRQTWSGPGTTKRFPETVLARCVKYTEIHPEMRHVDCQSVWDAFKGAFISKHPCDITEEDYQPLMKLGTQTVPCNKILLWSRIKDLAHQFTQVQRDMFTLEDTLLGYLADDLTWCGEFDTSKINYQSCPDWRKDCSNNPVSVFWKTVSRRFAEAACDVVHVMLDGSRSKIFDKDSTFGSVEVHNLQPEKVQTLEAWVIHGGREDSRDLCQDPTIKELESIISKRNIQFSCKNIYRPDKFLQCVKNPEDSSC 296
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Flavodoxin-like (1057)

Superfamily: N-(deoxy)ribosyltransferase-like (76)

Family: ADP ribosyl cyclase-like (60)

Protein domain: ADP ribosyl cyclase (42)

Human (Homo sapiens) [TaxId: 9606] (33)

1a	d4f46a_	A:
1b	d4f46b_	B:

(no "CATH Domain" information available for 4F46)

(no "Pfam Domain" information available for 4F46)

Asymmetric Unit(hide GO term definitions)

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4f45	CD38 E226Q MUTANT IN COMPLEX WITH NAADP

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (11, 11)

Cis Peptide Bonds (0, 0)

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SCOP Domains (1, 2)

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Gene Ontology (37, 37)

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