5AH4 - JenaLib

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

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

Date :   04 Feb 15 (Deposition) - 03 Jun 15 (Release) - 17 Jun 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.31

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, Dnan, Dna Polymerase, Tuberculosis (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_DNANMSM
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	MYCOBACTERIUM SMEGMATIS
	Organism Taxid	:	1772
	Strain	:	MC(2)155

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

		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 (7, 17)

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

Biological Unit 1 (6, 8)

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

Biological Unit 2 (6, 8)

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

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:327 , PRO A:328 , LEU A:329 , HOH A:2058	BINDING SITE FOR RESIDUE NA A1398
2	AC2	SOFTWARE	ARG A:181 , PHE A:182 , ARG A:183 , GLU A:255 , PRO A:257 , LYS A:258 , LEU A:262 , MET A:391 , PRO A:392 , VAL A:393 , ARG A:394 , HOH A:2023 , HOH A:2087 , HOH A:2088 , HOH A:2091 , HOH A:2092 , LEU B:159 , MLU D:10	BINDING SITE FOR CHAIN C OF CYCLOHEXYL GRISELIMYCIN
3	AC3	SOFTWARE	THR B:179 , ARG B:181 , PHE B:182 , ARG B:183 , GLU B:255 , LYS B:258 , LEU B:262 , MET B:391 , PRO B:392 , ARG B:394 , HOH B:2101 , HOH B:2102 , MLU C:10	BINDING SITE FOR CHAIN D OF CYCLOHEXYL GRISELIMYCIN

(no "SS Bond" information available for 5AH4)

Asymmetric Unit

No.	Residues
1	Gly A:377	-	Pro A:378
2	Gly B:377	-	Pro B:378

(no "SAP(SNP)/Variant" information available for 5AH4)

(no "PROSITE Motif" information available for 5AH4)

(no "Exon" information available for 5AH4)

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:380
                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeehhhhhhhhhhhhhhh.......eeeeee....eeeeee...eeeeeee..eeee.eeeeeehhhhhhhhhhh....eeeeee..eeeeee..eeeeee..hhhhh........eeeeehhhhhhhhhhhhhh.......hhhh.eeeeeee..eeeeeee...eeeeeeee.ee.....eeeeeeehhhhhhhhhh...eeee...........eeeeee..eeeeee........hhhhh..ee.eeeeeehhhhhhhhhhhhhhhhhhh.eeeeee..eeeeeeee...eeeeeeee.eeee..eeeeehhhhhhhhhhhh...eeeeee......eeeee............ee.....eeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ah4 A   9 TDLKFRVVREDFADAVAWVARSLPTRVLAGVLLTGTDEGLTISGFDYEVSAEVKVSAEIASAGSVLVSGRLLSDITKALPAKPVEVSVEGTRVSLTCGSARFSLPTLAVEDYPALPALPEETGVIASDLFAEAIGQVAVAAGRDDTLPMLTGIRVEISGESVVLAATDRFRLAVRELTWVTTAGDVEAAVLVPAKTLAEAAKAGNQVHLALGSGASVGKDGLLGIRSEGKRSTTRLLDAEFPKFRQLLPAEHTAVATIGVAELTEAIKRVALVADRGAQIRMEFSDDTLKLSAGADDVGRAEEDLPVDFAGEPLTIAFNPTYLTDGLGSLHSERVTFGFTTPSRPAVLRPAGEDDGAGGSGPFPAAKTDYVYLLMPVRLP 396
                                    18        28     || 42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212  ||   225       235       245       255       265       275       285       295       305       315       325       335       345       355       365      |376       386       396
                                                    34|                                                                                                                                                                             215|                                                                                                                                                      372|                      
                                                     39                                                                                                                                                                              219                                                                                                                                                       374

Chain B from PDB  Type:PROTEIN  Length:380
                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeehhhhhhhhhhhhhhh....hhhh.eeeeee....eeeeee...eeeeeee..eeee.eeeeeehhhhhhhhhh.....eeeeee..eeeeee..eeeeee.................eeeehhhhhhhhhhhhh.......hhhh.eeeeeee..eeeeeee...eeeeeeee.ee.....eeeeeeehhhhhhhhhhh..eeeee...........eeeeee..eeeeee........hhhhh..ee.eeeeeehhhhhhhhhhhhhhhhhhh.eeeeee..eeeeeeee...eeeeeeee.eeee..eeeeehhhhhhhhhh.....eeeeee......eeeeee........ee.....eeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ah4 B   9 TDLKFRVVREDFADAVAWVARSLPTRIPVLAGVLLTGTDEGLTISGFDYEVSAEVKVSAEIASAGSVLVSGRLLSDITKALPAKPVEVSVEGTRVSLTCGSARFSLPTLAVEDYPALPALPEETGVIASDLFAEAIGQVAVAAGRDDTLPMLTGIRVEISGESVVLAATDRFRLAVRELTWVTTAGDVEAAVLVPAKTLAEAAKAGTNQVHLALGSGASVGKDGLLGIRSEGKRSTTRLLDAEFPKFRQLLPAEHTAVATIGVAELTEAIKRVALVADRGAQIRMEFSDDTLKLSAGADDVGRAEEDLPVDFAGEPLTIAFNPTYLTDGLGSLHSERVTFGFTTPSRPAVLRPAGEDGGSGPFPAAKTDYVYLLMPVRLP 396
                                    18        28     || 40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210      |222       232       242       252       262       272       282       292       302       312       322       332       342       352       362      |376       386       396
                                                    34|                                                                                                                                                                                 217|                                                                                                                                                  369|                      
                                                     37                                                                                                                                                                                  220                                                                                                                                                   374

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
                 5ah4 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
                 5ah4 D   1 xvptLpLvpxG  11
                            |||| | |10 
                            |||| | ||| 
                            1-ACE| ||| 
                             2-MVA ||| 
                              3-MP8||| 
                               4-NZC|| 
                                 6-MP8 
                                   8-MVA
                                    9-PH6
                                    10-MLU

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 '\|'

(no "SCOP Domain" information available for 5AH4)

(no "CATH Domain" information available for 5AH4)

(no "Pfam Domain" information available for 5AH4)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		ACE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MLU	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MP8	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MVA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NZC	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PH6	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gly A:377 - Pro A:378	[ RasMol ]
		Gly B:377 - Pro B:378	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	A0QND6_MYCS2 \| A0QND6	:	5ah2

5agu	THE SLIDING CLAMP OF MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH A NATURAL PRODUCT.
5agv	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.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (7, 17)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

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Gene Ontology (10, 10)

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