2CBQ - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE NEOCARZINOSTATIN 1TES15 MUTANT BOUND TO TESTOSTERONE HEMISUCCINATE.

Authors :   A. Drevelle, M. Graille, B. Heyd, I. Sorel, N. Ulryck, F. Pecorari, M. Desmadril, H. Van Tilbeurgh, P. Minard

Date :   06 Jan 06 (Deposition) - 22 Mar 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Antibiotic, Antimicrobial, Dna-Binding, Phage-Display Hapten Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Drevelle, M. Graille, B. Heyd, I. Sorel, N. Ulryck, F. Pecorari, M. Desmadril, H. Van Tilbeurgh, P. Minard
Structures Of In Vitro Evolved Binding Sites On Neocarzinostatin Scaffold Reveal Unanticipated Evolutionary Pathways.
J. Mol. Biol. V. 358 455 2006
PubMed-ID: 16529771 | Reference-DOI: 10.1016/J.JMB.2006.02.002
(for further references see the PDB file header)

Molecule 1 - NEOCARZINOSTATIN
	Chains	:	A, B, C, D, E, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BLR(DE3) PLYSS
	Expression System Taxid	:	562
	Fragment	:	RESIDUES 35-147
	Mutation	:	YES
	Organism Scientific	:	STREPTOMYCES CARZINOSTATICUS
	Organism Taxid	:	1897
	Synonym	:	NCS, MITOMALCIN, MMC

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A		C
Biological Unit 2 (1x)	:		B				F
Biological Unit 3 (1x)	:				D	E

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 13)

No.	Name	Count	Type	Full Name
1	SO4	5	Ligand/Ion	SULFATE ION
2	TH2	8	Ligand/Ion	TESTOSTERONE HEMISUCCINATE

Biological Unit 1 (2, 5)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION
2	TH2	3	Ligand/Ion	TESTOSTERONE HEMISUCCINATE

Biological Unit 2 (2, 5)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION
2	TH2	3	Ligand/Ion	TESTOSTERONE HEMISUCCINATE

Biological Unit 3 (2, 3)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION
2	TH2	2	Ligand/Ion	TESTOSTERONE HEMISUCCINATE

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	SER A:14 , ASP A:15 , ARG A:71	BINDING SITE FOR RESIDUE SO4 A1113
02	AC2	SOFTWARE	ASP B:15 , ARG B:71 , ASN B:113	BINDING SITE FOR RESIDUE SO4 B1115
03	AC3	SOFTWARE	SER C:14 , ASP C:15 , ARG C:71 , ASN C:113	BINDING SITE FOR RESIDUE SO4 C1114
04	AC4	SOFTWARE	SER E:14 , ASP E:15 , ARG E:71	BINDING SITE FOR RESIDUE SO4 E1114
05	AC5	SOFTWARE	SER F:14 , ASP F:15 , ARG F:71	BINDING SITE FOR RESIDUE SO4 F1113
06	AC6	SOFTWARE	TRP A:33 , TYR A:35 , SER A:47 , PRO A:49 , ALA A:101 , GLY A:102 , TRP C:33	BINDING SITE FOR RESIDUE TH2 A1114
07	AC7	SOFTWARE	TRP A:83 , VAL A:86 , ASP A:87 , THR A:90 , ALA A:91 , THR F:8 , VAL F:18 , LYS F:20	BINDING SITE FOR RESIDUE TH2 A1115
08	AC8	SOFTWARE	THR B:8 , TRP B:33 , TYR B:35 , SER B:47 , PRO B:49 , ALA B:100 , ALA B:101 , GLY B:102	BINDING SITE FOR RESIDUE TH2 B1116
09	AC9	SOFTWARE	TRP B:83 , VAL B:86 , ASP B:87 , THR B:90 , ALA B:91 , THR C:8 , VAL C:18 , LYS C:20 , GLY E:43 , HIS E:45 , PHE E:78	BINDING SITE FOR RESIDUE TH2 B1117
10	BC1	SOFTWARE	HOH A:2010 , TRP C:33 , TYR C:35 , SER C:47 , PRO C:49 , SER C:98 , ALA C:101 , GLY C:102 , SER D:11	BINDING SITE FOR RESIDUE TH2 C1115
11	BC2	SOFTWARE	TRP D:33 , TYR D:35 , SER D:47 , PRO D:49 , SER D:98 , GLY D:102 , TH2 E:1115	BINDING SITE FOR RESIDUE TH2 D1114
12	BC3	SOFTWARE	SER C:11 , TH2 D:1114 , TRP E:33 , SER E:47 , PRO E:49 , LEU E:52 , PHE E:78 , ALA E:100 , GLY E:102	BINDING SITE FOR RESIDUE TH2 E1115
13	BC4	SOFTWARE	TRP F:33 , TYR F:35 , SER F:47 , PRO F:49 , ALA F:100	BINDING SITE FOR RESIDUE TH2 F1114

Asymmetric Unit

No.	Residues
1	A:88	-	A:93
2	B:88	-	B:93
3	C:88	-	C:93
4	D:88	-	D:93
5	E:88	-	E:93
6	F:88	-	F:93

Asymmetric Unit

No.	Residues
1	Thr A:8	-	Pro A:9
2	Thr B:8	-	Pro B:9
3	Thr C:8	-	Pro C:9
4	Thr D:8	-	Pro D:9
5	Thr E:8	-	Pro E:9
6	Thr F:8	-	Pro F:9

(no "SAP(SNP)/Variant" information available for 2CBQ)

(no "PROSITE Motif" information available for 2CBQ)

(no "Exon" information available for 2CBQ)

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:111
 aligned with NCZS_STRCZ | P0A3R9 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:111
                                    45        55        65        75        85        95       105       115       125       135       145 
           NCZS_STRCZ    36 APTATVTPSSGLSDGTVVKVAGAGLQAGTAYDVGQCAWVDTGVLACNPADFSSVTADANGSASTSLTVRRSFEGFLFDGTRWGTVDCTTAACQVGLSDAAGNGPEGVAISF 146
               SCOP domains d2cbqa_ A: automated matches                                                                                    SCOP domains
               CATH domains 2cbqA00 A:2-112  [code=2.60.40.230, no name defined]                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.........eeeeeee......eeeeeeeeeee..eeee.hhhheeee......eeeeee...eeeeee....eeeeee......eeeee.........ee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 2cbq A   2 APTATVTPSSGLSDGTVVKVAGAGLQAGTAYWVYQRAAVDTGVHASNPADLSSVTADANGSASTSLTVRRSFEGFLFDGTRWGTVDCTTAACQVGLSDAAGNGPEGVAISF 112
                                    11        21        31        41        51        61        71        81        91       101       111

Chain B from PDB  Type:PROTEIN  Length:113
 aligned with NCZS_STRCZ | P0A3R9 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:113
                                                                                                                                         147 
                                    45        55        65        75        85        95       105       115       125       135       145 | 
           NCZS_STRCZ    36 APTATVTPSSGLSDGTVVKVAGAGLQAGTAYDVGQCAWVDTGVLACNPADFSSVTADANGSASTSLTVRRSFEGFLFDGTRWGTVDCTTAACQVGLSDAAGNGPEGVAISFN-   -
               SCOP domains d2cbqb_ B: automated matches                                                                                      SCOP domains
               CATH domains 2cbqB00 B:2-114  [code=2.60.40.230, no name defined]                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.........eeeeeee......eeeeeeeeeee..eeee.hhhheeee......eeeeee...eeeee.....eeeeee.....eeeeee.........ee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 2cbq B   2 APTATVTPSSGLSDGTVVKVAGAGLQAGTAYWVYQRAAVDTGVHASNPADLSSVTADANGSASTSLTVRRSFEGFLFDGTRWGTVDCTTAACQVGLSDAAGNGPEGVAISFNH 114
                                    11        21        31        41        51        61        71        81        91       101       111

Chain C from PDB  Type:PROTEIN  Length:112
 aligned with NCZS_STRCZ | P0A3R9 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:112
                                    45        55        65        75        85        95       105       115       125       135       145  
           NCZS_STRCZ    36 APTATVTPSSGLSDGTVVKVAGAGLQAGTAYDVGQCAWVDTGVLACNPADFSSVTADANGSASTSLTVRRSFEGFLFDGTRWGTVDCTTAACQVGLSDAAGNGPEGVAISFN 147
               SCOP domains d2cbqc_ C: automated matches                                                                                     SCOP domains
               CATH domains 2cbqC00 C:2-113  [code=2.60.40.230, no name defined]                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.........eeeeeee......eeeeeeeeeee..eeee.hhhheeee......eeeeee...eeeeee....eeeeee.....eeeeee.........ee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 2cbq C   2 APTATVTPSSGLSDGTVVKVAGAGLQAGTAYWVYQRAAVDTGVHASNPADLSSVTADANGSASTSLTVRRSFEGFLFDGTRWGTVDCTTAACQVGLSDAAGNGPEGVAISFN 113
                                    11        21        31        41        51        61        71        81        91       101       111

Chain D from PDB  Type:PROTEIN  Length:112
 aligned with NCZS_STRCZ | P0A3R9 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:112
                                    45        55        65        75        85        95       105       115       125       135       145  
           NCZS_STRCZ    36 APTATVTPSSGLSDGTVVKVAGAGLQAGTAYDVGQCAWVDTGVLACNPADFSSVTADANGSASTSLTVRRSFEGFLFDGTRWGTVDCTTAACQVGLSDAAGNGPEGVAISFN 147
               SCOP domains d2cbqd_ D: automated matches                                                                                     SCOP domains
               CATH domains 2cbqD00 D:2-113  [code=2.60.40.230, no name defined]                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.........eeeeeee......eeeeeeeeeee..eeee.hhhheeee......eeeeee...eeeeee....eeeeee.....eeeeee.........ee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 2cbq D   2 APTATVTPSSGLSDGTVVKVAGAGLQAGTAYWVYQRAAVDTGVHASNPADLSSVTADANGSASTSLTVRRSFEGFLFDGTRWGTVDCTTAACQVGLSDAAGNGPEGVAISFN 113
                                    11        21        31        41        51        61        71        81        91       101       111

Chain E from PDB  Type:PROTEIN  Length:112
 aligned with NCZS_STRCZ | P0A3R9 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:112
                                    45        55        65        75        85        95       105       115       125       135       145  
           NCZS_STRCZ    36 APTATVTPSSGLSDGTVVKVAGAGLQAGTAYDVGQCAWVDTGVLACNPADFSSVTADANGSASTSLTVRRSFEGFLFDGTRWGTVDCTTAACQVGLSDAAGNGPEGVAISFN 147
               SCOP domains d2cbqe_ E: automated matches                                                                                     SCOP domains
               CATH domains 2cbqE00 E:2-113  [code=2.60.40.230, no name defined]                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.........eeeeeee......eeeeeeeeeee..eeee.hhhheeee......eeeeee...eeeeee....eeeeee.....eeeeee.........ee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 2cbq E   2 APTATVTPSSGLSDGTVVKVAGAGLQAGTAYWVYQRAAVDTGVHASNPADLSSVTADANGSASTSLTVRRSFEGFLFDGTRWGTVDCTTAACQVGLSDAAGNGPEGVAISFN 113
                                    11        21        31        41        51        61        71        81        91       101       111

Chain F from PDB  Type:PROTEIN  Length:111
 aligned with NCZS_STRCZ | P0A3R9 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:111
                                    45        55        65        75        85        95       105       115       125       135       145 
           NCZS_STRCZ    36 APTATVTPSSGLSDGTVVKVAGAGLQAGTAYDVGQCAWVDTGVLACNPADFSSVTADANGSASTSLTVRRSFEGFLFDGTRWGTVDCTTAACQVGLSDAAGNGPEGVAISF 146
               SCOP domains d2cbqf_ F: automated matches                                                                                    SCOP domains
               CATH domains 2cbqF00 F:2-112  [code=2.60.40.230, no name defined]                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.........eeeeeee......eeeeeeeeeee..eeee.hhhheeee.....eeeeeee...eeeee.....eeeeee.....eeeeee.........ee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 2cbq F   2 APTATVTPSSGLSDGTVVKVAGAGLQAGTAYWVYQRAAVDTGVHASNPADLSSVTADANGSASTSLTVRRSFEGFLFDGTRWGTVDCTTAACQVGLSDAAGNGPEGVAISF 112
                                    11        21        31        41        51        61        71        81        91       101       111

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: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: Actinoxanthin-like (17)

Family: Actinoxanthin-like (17)

Protein domain: automated matches (4)

Streptomyces carzinostaticus [TaxId: 1897] (4)

1a	d2cbqa_	A:
1b	d2cbqb_	B:
1c	d2cbqc_	C:
1d	d2cbqd_	D:
1e	d2cbqe_	E:
1f	d2cbqf_	F:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: [code=2.60.40.230, no name defined] (17)

Streptomyces carzinostaticus. Organism_taxid: 1897. (6)

1a	2cbqC00	C:2-113
1b	2cbqF00	F:2-112
1c	2cbqB00	B:2-114
1d	2cbqD00	D:2-113
1e	2cbqE00	E:2-113
1f	2cbqA00	A:2-112

(no "Pfam Domain" information available for 2CBQ)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F (NCZS_STRCZ | P0A3R9)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
	GO:0006952	defense response	Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
	GO:0042742	defense response to bacterium	Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Thr A:8 - Pro A:9	[ RasMol ]
		Thr B:8 - Pro B:9	[ RasMol ]
		Thr C:8 - Pro C:9	[ RasMol ]
		Thr D:8 - Pro D:9	[ RasMol ]
		Thr E:8 - Pro E:9	[ RasMol ]
		Thr F:8 - Pro F:9	[ RasMol ]

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	2cbq
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UniProtKB/Swiss-Prot
	NCZS_STRCZ \| P0A3R9	:	1j5h 1j5i 1nco 1noa 1o5p 2cbm 2cbo 2cbt 2g0k 2g0l

1j5h	SOLUTION STRUCTURE OF APO-NEOCARZINOSTATIN
1j5i	SOLUTION STRUCTURE OF A NOVEL CHROMOPROTEIN DERIVED FROMAPO-NEOCARZINOSTATIN AND A SYNTHETIC CHROMOPHORE
1kvh	NCSI-GB-BULGE-DNA COMPLEX INDUCED FORMATION OF A DNA BULGESTRUCTURE BY A MOLECULAR WEDGE LIGAND-POST-ACTIVATEDNEOCARZINOSTATIN CHROMOPHORE
1mp7	A THIRD COMPLEX OF POST-ACTIVATED NEOCARZINOSTATINCHROMOPHORE WITH DNA. BULGE DNA BINDING FROM THE MINORGROOVE
1nco	HOLO-NEOCARZINOSTATIN (CONTAINING CHROMOPHORE) COMPLEX WITH APO-CARZINOSTATIN (CONTAINING MPD)
1noa	NEOCARZINOSTATIN
1o5p	SOLUTION STRUCTURE OF HOLO-NEOCARZINOSTATIN
2cbm	CRYSTAL STRUCTURE OF THE APO-FORM OF A NEOCARZINOSTATIN MUTANT EVOLVED TO BIND TESTOSTERONE.
2cbo	CRYSTAL STRUCTURE OF THE NEOCARZINOSTATIN 3TES24 MUTANT BOUND TO TESTOSTERONE HEMISUCCINATE.
2cbt	CRYSTAL STRUCTURE OF THE NEOCARZINOSTATIN 4TES1 MUTANT BOUND TESTOSTERONE HEMISUCCINATE.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 13)

Sites (13, 13)

SS Bonds (6, 6)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (1, 6)

CATH Domains (1, 6)

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Gene Ontology (3, 3)

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