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Asym./Biol. Unit (Jmol Viewer)

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

Title :   E. COLI SLIDING CLAMP IN COMPLEX WITH (R)-9-(2-AMINO-2-OXOETHYL)-6-CHLORO-2,3,4,9-TETRAHYDRO-1H-CARBAZOLE-2-CARBOXYLIC ACID

Authors :   Z. Yin, A. J. Oakley

Date :   21 Feb 14 (Deposition) - 05 Mar 14 (Release) - 24 Jun 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Poliii Beta, Sliding Clamp, Dnan, Transferase, Transferase- Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Z. Yin, L. R. Whittell, Y. Wang, S. Jergic, C. Ma, P. J. Lewis, N. E. Dixon J. L. Beck, M. J. Kelso, A. J. Oakley
Bacterial Sliding Clamp Inhibitors That Mimic The Sequentia Binding Mechanism Of Endogenous Linear Motifs.
J. Med. Chem. V. 58 4693 2015
PubMed-ID: 25970224 | Reference-DOI: 10.1021/ACS.JMEDCHEM.5B00232

Molecule 1 - DNA POLYMERASE III SUBUNIT BETA
	Chains	:	A, B
	EC Number	:	2.7.7.7
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PND261
	Expression System Strain	:	AN1459
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	BN896_3391, DNAN
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	1403831
	Strain	:	K12 SUBSTR. MC4100

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (7, 16)

No.	Name	Count	Type	Full Name
1	2VF	2	Ligand/Ion	(2R)-9-(2-AMINO-2-OXOETHYL)-6-CHLORO-2,3,4,9-TETRAHYDRO-1H-CARBAZOLE-2-CARBOXYLIC ACID
2	CA	4	Ligand/Ion	CALCIUM ION
3	CL	2	Ligand/Ion	CHLORIDE ION
4	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
5	PEG	4	Ligand/Ion	DI(HYDROXYETHYL)ETHER
6	PG4	2	Ligand/Ion	TETRAETHYLENE GLYCOL
7	PGE	1	Ligand/Ion	TRIETHYLENE GLYCOL

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:152 , TYR A:154 , THR A:172 , GLY A:174 , ARG A:176 , LEU A:177 , PRO A:242 , VAL A:247 , VAL A:360 , MET A:362 , HOH A:658 , LYS B:250 , ASN B:251	BINDING SITE FOR RESIDUE 2VF A 401
02	AC2	SOFTWARE	ARG A:56 , VAL A:57 , ALA A:58 , ASP A:229	BINDING SITE FOR RESIDUE PEG A 402
03	AC3	SOFTWARE	GLU A:257 , THR A:309	BINDING SITE FOR RESIDUE PEG A 403
04	AC4	SOFTWARE	GLU A:334 , HOH A:699 , HOH A:736	BINDING SITE FOR RESIDUE CA A 404
05	AC5	SOFTWARE	ASP A:121 , TRP A:122 , ARG A:224 , GLN B:36	BINDING SITE FOR RESIDUE PG4 A 405
06	AC6	SOFTWARE	HOH A:563 , HOH A:697 , HOH A:737 , HOH A:738 , GLU B:163 , GLU B:166	BINDING SITE FOR RESIDUE CA A 406
07	AC7	SOFTWARE	THR A:110 , LEU A:111 , HOH A:633 , HOH A:636 , HOH A:727 , HOH A:728 , HOH A:734 , HOH A:735	BINDING SITE FOR RESIDUE CA A 407
08	AC8	SOFTWARE	SER A:181 , SER A:356	BINDING SITE FOR RESIDUE CA A 408
09	AC9	SOFTWARE	ASP A:261 , LYS A:264 , GLN A:265	BINDING SITE FOR RESIDUE EDO A 409
10	BC1	SOFTWARE	GLN A:265 , ARG A:269 , HOH A:550	BINDING SITE FOR RESIDUE CL A 410
11	BC2	SOFTWARE	ARG B:152 , TYR B:154 , THR B:172 , GLY B:174 , HIS B:175 , ARG B:176 , LEU B:177 , PRO B:242 , HOH B:681	BINDING SITE FOR RESIDUE 2VF B 401
12	BC3	SOFTWARE	GLN B:15 , GLN B:16 , GLU B:202 , ARG B:205	BINDING SITE FOR RESIDUE PEG B 402
13	BC4	SOFTWARE	THR B:129 , PRO B:213 , ARG B:215 , HIS B:226 , HOH B:503	BINDING SITE FOR RESIDUE PEG B 403
14	BC5	SOFTWARE	ASP B:121 , TRP B:122 , ARG B:224	BINDING SITE FOR RESIDUE PG4 B 404
15	BC6	SOFTWARE	SER B:18 , LEU B:21 , ARG B:73	BINDING SITE FOR RESIDUE PGE B 405
16	BC7	SOFTWARE	ASN B:275	BINDING SITE FOR RESIDUE CL B 406

(no "SS Bond" information available for 4OVG)

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

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

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

(no "Exon" information available for 4OVG)

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
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Chain A from PDB  Type:PROTEIN  Length:361
                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4ovga1 A:1-122 DNA polymerase III, beta subunit                                                                     d4ovga2 A:123-244 DNA polymerase III, beta subunit                                                                        d4ovga3 A:245-366 DNA polymerase III, beta subunit                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeehhhhhhhhhhhhh...hhh.eeeeeee..eeeeeee...eeeeeeee.......eeeeeehhhhhhhhhhh....eeeeeee..eeeeee..eeeeee..hhhhh.........eeeeehhhhhhhhhhhhhhhh.....hhhh.eeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeeeeeehhhhhhhhhhh......eeeee...eeeeee..eeeeee.......hhhhhh.....eeeeeehhhhhhhhhhhhh.......eeeeeee..eeeeeee.....eeeeeee.ee....eeeeeehhhhhhhhhhhh..eeeeee......eeeee..eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ovg A   1 MKFTVEREHLLKPLQQVSGPLGPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYVVMPMRL 366
                                    10        20 ||     35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365 
                                                22|                                                                                                                                                                                                                                                                                                                                                  
                                                 28

Chain B from PDB  Type:PROTEIN  Length:366
                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4ovgb1 B:1-122 DNA polymerase III, beta subunit                                                                          d4ovgb2 B:123-244 DNA polymerase III, beta subunit                                                                        d4ovgb3 B:245-366 DNA polymerase III, beta subunit                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeehhhhhhhhhhhhh.......hhhh.eeeeeee..eeeeeee...eeeeeeee.......eeeeeehhhhhhhhhhh....eeeeeee..eeeeee..eeeeee..hhhhh.........eeeeehhhhhhhhhhhhhhhh.....hhhh.eeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeeeeehhhhhhhhhhh......eeeee...eeeeee..eeeeee.......hhhhh......eeeeeehhhhhhhhhhhhh.......eeeeeee..eeeeeee.....eeeeeee.......eeeeeehhhhhhhhhhhh..eeeeee......eeeee.....eeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ovg B   1 MKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYVVMPMRL 366
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360

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/Biological Unit

Classes(

)

Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

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

Fold: DNA clamp (88)

Superfamily: DNA clamp (88)

Family: DNA polymerase III, beta subunit (31)

Protein domain: DNA polymerase III, beta subunit (31)

Escherichia coli [TaxId: 562] (30)

1a	d4ovga1	A:1-122
1b	d4ovgb2	B:123-244
1c	d4ovgb3	B:245-366
1d	d4ovga2	A:123-244
1e	d4ovga3	A:245-366
1f	d4ovgb1	B:1-122

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

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

Asymmetric/Biological Unit(hide GO term definitions)

(no "Gene Ontology" information available for 4OVG)

Asymmetric/Biological Unit
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Description

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Ligands, Modified Residues, Ions (7, 16)

Sites (16, 16)

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