5AGV - JenaLib

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Title :   THE SLIDING CLAMP OF MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH A NATURAL PRODUCT.

Authors :   P. Lukat, A. Kling, D. W. Heinz, R. Mueller

Date :   03 Feb 15 (Deposition) - 03 Jun 15 (Release) - 14 Jun 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.93

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

Keywords :   Transferase-Antibiotic Complex, Transferase, Dnan, Natural Product, Sliding Clamp (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Kling, P. Lukat, D. V. Almeida, A. Bauer, E. Fontaine, S. Sordello, N. Zaburannyi, J. Herrmann, S. C. Wenzel, C. Konig, N. C. Ammerman, M. B. Barrio, K. Borchers, F. Bordon-Pallier, M. Bronstrup, G. Courtemanche, M. Gerlitz, M. Geslin, P. Hammann, D. W. Heinz, H. Hoffmann, S. Klieber, M. Kohlmann, M. Kurz, C. Lair, H. Matter, E. Nuermberger, S. Tyagi, L. Fraisse, J. H. Grosset, S. Lagrange, R. Muller
Antibiotics. Targeting Dnan For Tuberculosis Therapy Using Novel Griselimycins.
Science V. 348 1106 2015
PubMed-ID: 26045430 | Reference-DOI: 10.1126/SCIENCE.AAA4690

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	:	PVP008_DNANMTB
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS H37RV
	Organism Taxid	:	83332

Molecule 2 - CYCLOHEXYL GRISELIMYCIN
	Chains	:	C, D
	Organism Scientific	:	STREPTOMYCES CAELICUS
	Organism Taxid	:	1520516

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (9, 39)

No.	Name	Count	Type	Full Name
1	ACE	2	Mod. Amino Acid	ACETYL GROUP
2	BU3	5	Ligand/Ion	(R,R)-2,3-BUTANEDIOL
3	CA	6	Ligand/Ion	CALCIUM ION
4	MLU	2	Mod. Amino Acid	N-METHYL-D-LEUCINE
5	MP8	4	Mod. Amino Acid	(4R)-4-METHYL-L-PROLINE
6	MVA	4	Mod. Amino Acid	N-METHYLVALINE
7	NA	12	Ligand/Ion	SODIUM ION
8	NZC	2	Mod. Amino Acid	N-METHYLIDENE-L-THREONINE
9	PH6	2	Mod. Amino Acid	(4S)-4-CYCLOHEXYL-L-PROLINE

Biological Unit 1 (7, 10)

No.	Name	Count	Type	Full Name
1	ACE	1	Mod. Amino Acid	ACETYL GROUP
2	BU3	2	Ligand/Ion	(R,R)-2,3-BUTANEDIOL
3	CA	-1	Ligand/Ion	CALCIUM ION
4	MLU	1	Mod. Amino Acid	N-METHYL-D-LEUCINE
5	MP8	2	Mod. Amino Acid	(4R)-4-METHYL-L-PROLINE
6	MVA	2	Mod. Amino Acid	N-METHYLVALINE
7	NA	-1	Ligand/Ion	SODIUM ION
8	NZC	1	Mod. Amino Acid	N-METHYLIDENE-L-THREONINE
9	PH6	1	Mod. Amino Acid	(4S)-4-CYCLOHEXYL-L-PROLINE

Biological Unit 2 (7, 11)

No.	Name	Count	Type	Full Name
1	ACE	1	Mod. Amino Acid	ACETYL GROUP
2	BU3	3	Ligand/Ion	(R,R)-2,3-BUTANEDIOL
3	CA	-1	Ligand/Ion	CALCIUM ION
4	MLU	1	Mod. Amino Acid	N-METHYL-D-LEUCINE
5	MP8	2	Mod. Amino Acid	(4R)-4-METHYL-L-PROLINE
6	MVA	2	Mod. Amino Acid	N-METHYLVALINE
7	NA	-1	Ligand/Ion	SODIUM ION
8	NZC	1	Mod. Amino Acid	N-METHYLIDENE-L-THREONINE
9	PH6	1	Mod. Amino Acid	(4S)-4-CYCLOHEXYL-L-PROLINE

Asymmetric Unit (25, 25)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	THR A:389 , BU3 A:508 , HOH A:823 , HOH A:832 , HOH A:849 , HOH A:897 , HOH A:917	binding site for residue CA A 501
02	AC2	SOFTWARE	HIS A:269 , HOH A:702 , HOH A:762 , HOH A:803	binding site for residue NA A 502
03	AC3	SOFTWARE	ASP A:292 , HOH A:687 , HOH A:916 , HOH A:967	binding site for residue NA A 503
04	AC4	SOFTWARE	SER A:249	binding site for residue NA A 504
05	AC5	SOFTWARE	LEU A:240 , ILE A:242 , SER A:249 , THR A:250 , THR A:251	binding site for residue NA A 505
06	AC6	SOFTWARE	ARG A:84 , LEU A:85 , ASP A:88 , HOH A:1019	binding site for residue NA A 506
07	AC7	SOFTWARE	THR A:120 , HOH A:691 , HOH A:889 , HOH A:942 , HOH A:950 , HOH A:1036	binding site for residue NA A 507
08	AC8	SOFTWARE	VAL A:188 , GLU A:190 , THR A:389 , ASP A:390 , TYR A:391 , CA A:501 , HOH A:666 , HOH A:823 , HOH A:832 , HOH A:849	binding site for residue BU3 A 508
09	AC9	SOFTWARE	ALA A:214 , GLY A:218 , GLY A:244 , ASN A:245 , LYS A:247 , HOH A:655	binding site for residue BU3 A 509
10	AD1	SOFTWARE	ARG A:16 , GLU A:72 , HOH A:748 , ARG B:16 , LEU B:17 , GLU B:72	binding site for residue BU3 A 510
11	AD2	SOFTWARE	GLY A:220 , GLY A:221 , HOH A:624 , GLU B:142 , HOH B:768	binding site for residue NA B 501
12	AD3	SOFTWARE	NA B:507 , HOH B:670 , HOH B:765 , HOH B:977 , HOH B:987 , HOH B:1078	binding site for residue CA B 502
13	AD4	SOFTWARE	THR B:389 , BU3 B:513 , HOH B:762 , HOH B:862 , HOH B:879 , HOH B:961 , HOH B:968	binding site for residue CA B 503
14	AD5	SOFTWARE	ASN B:379 , GLY B:380 , HOH B:710 , HOH B:776 , HOH B:801 , HOH B:836	binding site for residue CA B 504
15	AD6	SOFTWARE	LEU B:33 , ALA B:35 , BU3 B:512 , HOH B:636 , HOH B:682 , HOH B:741	binding site for residue CA B 505
16	AD7	SOFTWARE	ARG B:366 , VAL B:387 , HOH B:802 , HOH B:830	binding site for residue CA B 506
17	AD8	SOFTWARE	ASP B:325 , TYR B:326 , CA B:502 , HOH B:977 , HOH B:987	binding site for residue NA B 507
18	AD9	SOFTWARE	SER B:21 , ASP B:24 , VAL B:69 , HOH B:627 , HOH B:780 , HOH B:950	binding site for residue NA B 508
19	AE1	SOFTWARE	THR B:55 , SER B:57 , GLU B:66 , HOH B:808 , HOH B:996	binding site for residue NA B 509
20	AE2	SOFTWARE	GLY B:294 , ASN B:336 , THR B:338 , HOH B:1020	binding site for residue NA B 510
21	AE3	SOFTWARE	GLU B:282	binding site for residue NA B 511
22	AE4	SOFTWARE	LEU B:33 , GLY B:44 , VAL B:45 , CA B:505 , HOH B:628 , HOH B:636 , HOH B:669 , HOH B:682	binding site for residue BU3 B 512
23	AE5	SOFTWARE	VAL B:188 , GLU B:190 , ARG B:262 , THR B:389 , ASP B:390 , TYR B:391 , CA B:503 , HOH B:762 , HOH B:767 , HOH B:862 , HOH B:879	binding site for residue BU3 B 513
24	AE6	SOFTWARE	ARG A:183 , NZC C:4 , LEU C:5 , LEU C:7 , PH6 C:9 , MLU D:10	binding site for Di-peptide MLU C 10 and GLY C 11
25	AE7	SOFTWARE	ARG B:183 , MLU C:10 , NZC D:4 , LEU D:5 , LEU D:7 , PH6 D:9	binding site for Di-peptide MLU D 10 and GLY D 11

(no "SS Bond" information available for 5AGV)

Asymmetric Unit

No.	Residues
1	Gly A:382	-	Pro A:383
2	Gly B:382	-	Pro B:383
3	Mva C:8	-	Ph6 C:9
4	Mva D:8	-	Ph6 D:9

(no "SAP(SNP)/Variant" information available for 5AGV)

(no "PROSITE Motif" information available for 5AGV)

(no "Exon" information available for 5AGV)

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:390
                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeehhhhhhhhhhhhh.......hhhh.eeeeeee..eeeeee....eeeeeeee.eeee.eeeeeehhhhhhhhhhh...eeeeeee..eeeeee..eeeeee..hhhhh........eeeeehhhhhhhhhhhhhh.......hhhh.eeeeeee..eeeeeee...eeeeeeee.ee.....eeeeeeehhhhhhhhhhhh....eeee..hhhhh....eeeeee..eeeeee........hhhhh..ee.eeeeeehhhhhhhhhhhhhhh.....eeeeee..eeeeeeee...eeeeeeee.eeee..eeeeehhhhhhhhhhhh...eeeeee......eeeeee............ee.....eeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5agv A  10 LTDLTFRLLRESFADAVSWVAKNLPARPAVPVLSGVLLTGSDNGLTISGFDYEVSAEAQVGAEIVSPGSVLVSGRLLSDITRALPNKPVDVHVEGNRVALTCGNARFSLPTMPVEDYPTLPTLPEETGLLPAELFAEAISQVAIAAGRDDTLPMLTGIRVEILGETVVLAATDRFRLAVRELKWSASSPDIEAAVLVPAKTLAEAAKAGIGGSDVRLSLGTGPGVGKDGLLGISGNGKRSTTRLLDAEFPKFRQLLPTEHTAVATMDVAELIEAIKLVALVADRGAQVRMEFADGSVRLSAGADDVGRAEEDLVVDYAGEPLTIAFNPTYLTDGLSSLRSERVSFGFTTAGKPALLRPVSGDDRPLNGNGPFPAVSTDYVYLLMPVRLPG 402
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369    || 382       392       402
                                                                                                                                                                                                                                                                                                                                                                                                      374|                        
                                                                                                                                                                                                                                                                                                                                                                                                       378

Chain B from PDB  Type:PROTEIN  Length:393
                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeehhhhhhhhhhhhhhh.....hhhh.eeeeeee..eeeeeee...eeeeeeee.eeee.eeeeeehhhhhhhhhhh...eeeeeee..eeeeee..eeeeee...............eeeeeehhhhhhhhhhhhh.......hhhh.eeeeee...eeeeeee...eeeeeeee.ee......eeeeee..hhhhhh.......eeeee...........eeeeee..eeeeee........hhhhh..ee.eeeeeehhhhhhhhhhhhhhhhhhh.eeeeee..eeeeeeee...eeeeeeee.eee...eeeeehhhhhhhhhhhh...eeeeee......eeeee................ee.....eeeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5agv B  10 LTDLTFRLLRESFADAVSWVAKNLPARPAVPVLSGVLLTGSDNGLTISGFDYEVSAEAQVGAEIVSPGSVLVSGRLLSDITRALPNKPVDVHVEGNRVALTCGNARFSLPTMPVEDYPTLPTLPEETGLLPAELFAEAISQVAIAAGRDDTLPMLTGIRVEILGETVVLAATDRFRLAVRELKWSASSPDIEAAVLVPAKTLAEAAKAGIGGSDVRLSLGTGPGVGKDGLLGISGNGKRSTTRLLDAEFPKFRQLLPTEHTAVATMDVAELIEAIKLVALVADRGAQVRMEFADGSVRLSAGADDVGRAEEDLVVDYAGEPLTIAFNPTYLTDGLSSLRSERVSFGFTTAGKPALLRPVSGDDRPVAGLNGNGPFPAVSTDYVYLLMPVRLPG 402
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399

Chain C from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ........... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 5agv C   1 xvptLpLvpxG  11
                            |||| | |10 
                            1-ACE| ||| 
                             2-MVA ||| 
                              3-MP8||| 
                               4-NZC|| 
                                 6-MP8 
                                   8-MVA
                                    9-PH6
                                    10-MLU

Chain D from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ........... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 5agv D   1 xvptLpLvpxG  11
                            |||| | |10 
                            |||| | ||| 
                            1-ACE| ||| 
                             2-MVA ||| 
                              3-MP8||| 
                               4-NZC|| 
                                 6-MP8 
                                   8-MVA
                                    9-PH6
                                    10-MLU

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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 '\|'

(no "SCOP Domain" information available for 5AGV)

(no "CATH Domain" information available for 5AGV)

(no "Pfam Domain" information available for 5AGV)

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	Cis Peptide Bonds
		Gly A:382 - Pro A:383	[ RasMol ]
		Gly B:382 - Pro B:383	[ RasMol ]
		Mva C:8 - Ph6 C:9	[ RasMol ]
		Mva D:8 - Ph6 D:9	[ RasMol ]

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	DPO3B_MYCTU \| P9WNU1	:	3p16 3rb9 5agu
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5agu	THE SLIDING CLAMP OF MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH A NATURAL PRODUCT.
5ah2	THE SLIDING CLAMP OF MYCOBACTERIUM SMEGMATIS IN COMPLEX WITH A NATURAL PRODUCT.
5ah4	THE SLIDING CLAMP OF MYCOBACTERIUM SMEGMATIS IN COMPLEX WITH A NATURAL PRODUCT.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (9, 39)

Sites (25, 25)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (12, 22)

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Related Entries

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Related Entries Specified in the PDB File