5K82 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A PRIMATE APOBEC3G N-TERMINAL DOMAIN

Authors :   X. Xiao, S. -X. Li, H. Yang, X. S. Chen

Date :   27 May 16 (Deposition) - 10 Aug 16 (Release) - 10 Aug 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.91

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

Keywords :   Apobec3G, Vif, Hiv, Apobec, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Xiao, S. X. Li, H. Yang, X. S. Chen
Crystal Structures Of Apobec3G N-Domain Alone And Its Complex With Dna.
Nat Commun V. 7 12193 2016
PubMed-ID: 27480941 | Reference-DOI: 10.1038/NCOMMS12193

Molecule 1 - APOLIPOPROTEIN B MRNA EDITING ENZYME, CATALYTIC PEPTIDE- LIKE 3G,APOLIPOPROTEIN B MRNA EDITING ENZYME, CATALYTIC PEPTIDE-LIKE 3G
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI K-12
	Expression System Plasmid	:	PGEX6P-1
	Expression System Taxid	:	83333
	Fragment	:	UNP RESIDUES 1-195 (139CQKRDGPH146 REPLACED BY AEAG)
	Gene	:	APOBEC3G
	Organism Common	:	RHESUS MACAQUE
	Organism Scientific	:	MACACA MULATTA
	Organism Taxid	:	9544

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

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

Biological Unit 2 (0, 0)

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

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:65 , GLU A:67 , CYS A:97 , CYS A:100	binding site for residue ZN A 401
2	AC2	SOFTWARE	HIS B:65 , GLU B:67 , CYS B:97 , CYS B:100	binding site for residue ZN B 401
3	AC3	SOFTWARE	HIS C:65 , CYS C:97 , CYS C:100	binding site for residue ZN C 401
4	AC4	SOFTWARE	HIS D:65 , GLU D:67 , CYS D:97 , CYS D:100	binding site for residue ZN D 401

(no "SS Bond" information available for 5K82)

Asymmetric Unit

No.	Residues
1	Pro A:60	-	Lys A:61
2	Pro B:60	-	Lys B:61
3	Pro C:60	-	Lys C:61
4	Pro D:60	-	Lys D:61

(no "SAP(SNP)/Variant" information available for 5K82)

(no "PROSITE Motif" information available for 5K82)

(no "Exon" information available for 5K82)

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:188
                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhh..........eeeeeeee..........eeeeeeee...hhhhhhhhhhhhhhhhhhhh.....ee..eee....hhhhhhhhhhhhhhh..ee.eeee.......hhhhhhhhhhhhhhhheeee.hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k82 A   4 QIRNMVEPMDPRTFVSNFNNRPILSGLDTVWLCCEVKTKDPSGPPLDAKIFQGKVYPKAKYHPEMRFLRWFHKWRQLHHDQEYKVTWYVSWSPCTRCANSVATFLAKDPKVTLTIFVARLYYFWKPDYQQALRILAEAGATMKIMNYNEFQDCWNKFVDGRGKPFKPWNNLPKHYTLLQATLGELLRH 195
                                    13        23        33        43        53        63        73        83        93       103       113       123       133    || 147       157       167       177       187        
                                                                                                                                                                138|                                                    
                                                                                                                                                                 143

Chain B from PDB  Type:PROTEIN  Length:188
                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhh..........eeeee................eeeee...hhhhhhhhhhhhhhhhhhhhh....ee..eeeee..hhhhhhhhhhhhhhh..ee.eeeeee.....hhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k82 B   4 QIRNMVEPMDPRTFVSNFNNRPILSGLDTVWLCCEVKTKDPSGPPLDAKIFQGKVYPKAKYHPEMRFLRWFHKWRQLHHDQEYKVTWYVSWSPCTRCANSVATFLAKDPKVTLTIFVARLYYFWKPDYQQALRILAEAGATMKIMNYNEFQDCWNKFVDGRGKPFKPWNNLPKHYTLLQATLGELLRH 195
                                    13        23        33        43        53        63        73        83        93       103       113       123       133    || 147       157       167       177       187        
                                                                                                                                                                138|                                                    
                                                                                                                                                                 143

Chain C from PDB  Type:PROTEIN  Length:188
                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhh..........eeeee................eeeee...hhhhhhhhhhhhhhhhhhhhh....ee..eeeee..hhhhhhhhhhhhhhh..ee.eeeeee.....hhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k82 C   4 QIRNMVEPMDPRTFVSNFNNRPILSGLDTVWLCCEVKTKDPSGPPLDAKIFQGKVYPKAKYHPEMRFLRWFHKWRQLHHDQEYKVTWYVSWSPCTRCANSVATFLAKDPKVTLTIFVARLYYFWKPDYQQALRILAEAGATMKIMNYNEFQDCWNKFVDGRGKPFKPWNNLPKHYTLLQATLGELLRH 195
                                    13        23        33        43        53        63        73        83        93       103       113       123       133    || 147       157       167       177       187        
                                                                                                                                                                138|                                                    
                                                                                                                                                                 143

Chain D from PDB  Type:PROTEIN  Length:191
                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhh..........eeeee................eeeee...hhhhhhhhhhhhhhhhhhh......ee..eeeee..hhhhhhhhhhhhhhh..ee.eeeeee.....hhhhhhhhhhhhhhh.eeee.hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k82 D   1 MKPQIRNMVEPMDPRTFVSNFNNRPILSGLDTVWLCCEVKTKDPSGPPLDAKIFQGKVYPKAKYHPEMRFLRWFHKWRQLHHDQEYKVTWYVSWSPCTRCANSVATFLAKDPKVTLTIFVARLYYFWKPDYQQALRILAEAGATMKIMNYNEFQDCWNKFVDGRGKPFKPWNNLPKHYTLLQATLGELLRH 195
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       144       154       164       174       184       194 
                                                                                                                                                                   138|                                                    
                                                                                                                                                                    143

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 '\|'

(no "SCOP Domain" information available for 5K82)

(no "CATH Domain" information available for 5K82)

(no "Pfam Domain" information available for 5K82)

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	Cis Peptide Bonds
		Pro A:60 - Lys A:61	[ RasMol ]
		Pro B:60 - Lys B:61	[ RasMol ]
		Pro C:60 - Lys C:61	[ RasMol ]
		Pro D:60 - Lys D:61	[ RasMol ]

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		Biological Unit 2	[ Jena3D ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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