5CZ2 - JenaLib

Asymmetric Unit (Jmol Viewer)

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 A TWO-DOMAIN FRAGMENT OF MMTV INTEGRASE

Authors :   N. Cook, A. Ballandras-Colas, A. Engelman, P. Cherepanov

Date :   31 Jul 15 (Deposition) - 17 Feb 16 (Release) - 02 Mar 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.72

Chains :   Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,G,H  (1x)
Biol. Unit 2: C,D,K,L  (1x)
Biol. Unit 3: E,F,I,J  (1x)

Keywords :   Integrase, Pol, Retrovirus, Amino Terminal Domain, Catalytic Core Domain, Zinc Binding, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Ballandras-Colas, M. Brown, N. J. Cook, T. G. Dewdney, B. Demeler, P. Cherepanov, D. Lyumkis, A. N. Engelman
Cryo-Em Reveals A Novel Octameric Integrase Structure For Betaretroviral Intasome Function.
Nature V. 530 358 2016
PubMed-ID: 26887496 | Reference-DOI: 10.1038/NATURE16955

Molecule 1 - POL POLYPROTEIN
	Chains	:	A, B, C, D, E, F, G, H, I, J, K, L
	EC Number	:	2.7.7.49, 2.7.7.7, 3.1.26.4, 2.7.7.-, 3.1.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PCPH6P
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 1437-1646
	Gene	:	POL
	Organism Common	:	MMTV
	Organism Scientific	:	MOUSE MAMMARY TUMOR VIRUS (STRAIN BR6)
	Organism Taxid	:	11758
	Strain	:	BR6

		1	2	3	4	5	6	7	8	9	10	11	12
Asymmetric Unit	:	A	B	C	D	E	F	G	H	I	J	K	L
Biological Unit 1 (1x)	:	A	B					G	H
Biological Unit 2 (1x)	:			C	D							K	L
Biological Unit 3 (1x)	:					E	F			I	J

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 12)

No.	Name	Count	Type	Full Name
1	MG	6	Ligand/Ion	MAGNESIUM ION
2	ZN	6	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:65 , ASP A:122	binding site for residue MG A 301
02	AC2	SOFTWARE	ASP B:65 , ASP B:122	binding site for residue MG B 301
03	AC3	SOFTWARE	ASP C:65 , ASP C:122	binding site for residue MG C 301
04	AC4	SOFTWARE	ASP D:65 , ASP D:122	binding site for residue MG D 301
05	AC5	SOFTWARE	ASP E:65 , ASP E:122	binding site for residue MG E 301
06	AC6	SOFTWARE	ASP F:65 , ASP F:122	binding site for residue MG F 301
07	AC7	SOFTWARE	HIS G:9 , HIS G:13 , CYS G:37 , CYS G:40	binding site for residue ZN G 301
08	AC8	SOFTWARE	HIS H:9 , HIS H:13 , CYS H:37 , CYS H:40	binding site for residue ZN H 301
09	AC9	SOFTWARE	HIS I:9 , HIS I:13 , CYS I:37 , CYS I:40	binding site for residue ZN I 301
10	AD1	SOFTWARE	HIS J:9 , HIS J:13 , CYS J:37 , CYS J:40	binding site for residue ZN J 301
11	AD2	SOFTWARE	HIS K:9 , HIS K:13 , CYS K:37 , CYS K:40	binding site for residue ZN K 301
12	AD3	SOFTWARE	HIS L:9 , HIS L:13 , CYS L:37 , CYS L:40	binding site for residue ZN L 301

(no "SS Bond" information available for 5CZ2)

(no "Cis Peptide Bond" information available for 5CZ2)

(no "SAP(SNP)/Variant" information available for 5CZ2)

(no "PROSITE Motif" information available for 5CZ2)

(no "Exon" information available for 5CZ2)

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:151
                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeee.hhhhhh.eeeeeee.....eeeeee...hhhhhhhhhhhhhhhhh...eee........hhhhhhhhhhh..eee..hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.......hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cz2 A  51 VNPRGLKPRVLWQMDVTHVSEFGKLKYVHVTVDTYSHFTFATARTGEATKDVLQHLAQSFAYMGIPQKIKTDNAPAYVSRSIQEFLARWKISHVTQAIVERTHQNIKAQLNKLQKAGKYYTPHHLLAHALFVLNHVNMDNQGHTAAERHWG 209
                                    60        70        80        90       100       110       120       130       140    || 158       168       178       188       198       208 
                                                                                                                        145|                                                       
                                                                                                                         154

Chain B from PDB  Type:PROTEIN  Length:142
                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeee.hhhhhh.eeeeeee.....eeeeee...hhhhhhhhhhhhhhhhh...eee........hhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.......hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cz2 B  56 LKPRVLWQMDVTHVSEFGKLKYVHVTVDTYSHFTFATARTGEATKDVLQHLAQSFAYMGIPQKIKTDNAPAYVSRSIQEFLARWKISHVQAIVERTHQNIKAQLNKLQKYYTPHHLLAHALFVLNHVNMDNQGHTAAERHWG 209
                                    65        75        85        95       105       115       125       135       154       164       177       187       197       207  
                                                                                                                  144|               172|                                 
                                                                                                                   154                176

Chain C from PDB  Type:PROTEIN  Length:152
                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeeee.hhhhhh.eeeeeee.....eeeeee...hhhhhhhhhhhhhhhhh...eee........hhhhhhhhhhh..eee..hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.......hhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cz2 C  50 GVNPRGLKPRVLWQMDVTHVSEFGKLKYVHVTVDTYSHFTFATARTGEATKDVLQHLAQSFAYMGIPQKIKTDNAPAYVSRSIQEFLARWKISHVTQAIVERTHQNIKAQLNKLQKAGKYYTPHHLLAHALFVLNHVNMDNQGHTAAERHWG 209
                                    59        69        79        89        99       109       119       129       139     ||157       167       177       187       197       207  
                                                                                                                         145|                                                       
                                                                                                                          154

Chain D from PDB  Type:PROTEIN  Length:139
                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeee.hhhhhh.eeeeeee.....eeeeee...hhhhhhhhhhhhhhhhh...eee........hhhhhhhhhhh..eee.hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.......hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cz2 D  56 LKPRVLWQMDVTHVSEFGKLKYVHVTVDTYSHFTFATARTGEATKDVLQHLAQSFAYMGIPQKIKTDNAPAYVSRSIQEFLARWKISHVVERTHQNIKAQLNKLQKYYTPHHLLAHALFVLNHVNMDNQGHTAAERHWG 209
                                    65        75        85        95       105       115       125       135       157       167    || 180       190       200         
                                                                                                                  144|            172|                                 
                                                                                                                   157             176

Chain E from PDB  Type:PROTEIN  Length:153
                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeee.hhhhhh.eeeeeee.....eeeeee...hhhhhhhhhhhhhhhhh...eee........hhhhhhhhhhh..eee....hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.......hhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cz2 E  51 VNPRGLKPRVLWQMDVTHVSEFGKLKYVHVTVDTYSHFTFATARTGEATKDVLQHLAQSFAYMGIPQKIKTDNAPAYVSRSIQEFLARWKISHVTGIQAIVERTHQNIKAQLNKLQKAGKYYTPHHLLAHALFVLNHVNMDNQGHTAAERHWG 209
                                    60        70        80        90       100       110       120       130       140      |156       166       176       186       196       206   
                                                                                                                          147|                                                       
                                                                                                                           154

Chain F from PDB  Type:PROTEIN  Length:115
                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee...eeeee.....eeee.hhhhhhhhhhhhh...eee........hhhhhhhhhh.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.......hhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 5cz2 F  56 LKPRVLWQMDVTVHVTVDTYSHFTFATDVLQHLAQSFAYMGIPQKIKTDNAPAYVSRSIQEFLARVERTHQNIKAQLNKLQKKYYTPHHLLAHALFVLNHVNMDNQGHTAAERHW 208
                                    65 ||     85      |103       113       123       133    || 161       171 ||    183       193       203     
                                      67|            92|                                  138|             173|                                
                                       78            101                                   157              176

Chain G from PDB  Type:PROTEIN  Length:41
                                                                         
               SCOP domains ----------------------------------------- SCOP domains
               CATH domains ----------------------------------------- CATH domains
               Pfam domains ----------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------- PROSITE
                 Transcript ----------------------------------------- Transcript
                 5cz2 G   1 ALESAQESHALHHQNAAALRFQFHITREQAREIVKLCPNCP  41
                                    10        20        30        40

Chain H from PDB  Type:PROTEIN  Length:40
                                                                        
               SCOP domains ---------------------------------------- SCOP domains
               CATH domains ---------------------------------------- CATH domains
               Pfam domains ---------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------- PROSITE
                 Transcript ---------------------------------------- Transcript
                 5cz2 H   2 LESAQESHALHHQNAAALRFQFHITREQAREIVKLCPNCP  41
                                    11        21        31        41

Chain I from PDB  Type:PROTEIN  Length:39
                                                                       
               SCOP domains --------------------------------------- SCOP domains
               CATH domains --------------------------------------- CATH domains
               Pfam domains --------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------- PROSITE
                 Transcript --------------------------------------- Transcript
                 5cz2 I   3 ESAQESHALHHQNAAALRFQFHITREQAREIVKLCPNCP  41
                                    12        22        32

Chain J from PDB  Type:PROTEIN  Length:41
                                                                         
               SCOP domains ----------------------------------------- SCOP domains
               CATH domains ----------------------------------------- CATH domains
               Pfam domains ----------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------- PROSITE
                 Transcript ----------------------------------------- Transcript
                 5cz2 J   1 ALESAQESHALHHQNAAALRFQFHITREQAREIVKLCPNCP  41
                                    10        20        30        40

Chain K from PDB  Type:PROTEIN  Length:36
                                                                    
               SCOP domains ------------------------------------ SCOP domains
               CATH domains ------------------------------------ CATH domains
               Pfam domains ------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhh........hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------ PROSITE
                 Transcript ------------------------------------ Transcript
                 5cz2 K   2 LESAQESHALHHQNRFQFHITREQAREIVKLCPNCP  41
                                    11   ||   25        35      
                                        15|                     
                                         20

Chain L from PDB  Type:PROTEIN  Length:41
                                                                         
               SCOP domains ----------------------------------------- SCOP domains
               CATH domains ----------------------------------------- CATH domains
               Pfam domains ----------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------- PROSITE
                 Transcript ----------------------------------------- Transcript
                 5cz2 L   1 ALESAQESHALHHQNAAALRFQFHITREQAREIVKLCPNCP  41
                                    10        20        30        40

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 5CZ2)

(no "CATH Domain" information available for 5CZ2)

(no "Pfam Domain" information available for 5CZ2)

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	Ligands, Modified Residues, Ions
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	5cz2
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	POL_MMTVB \| P03365
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	2.7.7.49
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	POL_MMTVB \| P03365	:	3jca 5cz1 5d7u

(no "Related Entries Specified in the PDB File" available for 5CZ2)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 12)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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Gene Ontology (21, 21)

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