4R44 - JenaLib

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Description

Title :   RACEMIC CRYSTAL STRUCTURE OF A TETRAMOLECULAR DNA G-QUADRUPLEX

Authors :   P. K. Mandal, G. W. Collie, B. Kauffmann, I. Huc

Date :   19 Aug 14 (Deposition) - 12 Nov 14 (Release) - 14 Jan 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.69

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

Keywords :   Racemic Dna, Racemates, Dna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. K. Mandal, G. W. Collie, B. Kauffmann, I. Huc
Racemic Dna Crystallography.
Angew. Chem. Int. Ed. Engl. V. 53 14424 2014
PubMed-ID: 25358289 | Reference-DOI: 10.1002/ANIE.201409014

Compounds

*Molecule 1 - 5'-D(TPGPGPGPGPT)-3'*
	Chains	:	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
	Engineered	:	YES
	Organism Scientific	:	SYNTHETIC CONSTRUCT
	Organism Taxid	:	32630
	Other Details	:	TETRAMOLECULAR G-QUADRUPLEX
	Synthetic	:	YES

Structural Features

Chains, Units

		1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16
Asymmetric Unit	:	A	B	C	D	E	F	G	H	I	J	K	L	M	N	O	P
Biological Unit 1 (1x)	:	A	B	C	D	E	F	G	H
Biological Unit 2 (1x)	:									I	J	K	L	M	N	O	P

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (2, 18)

Asymmetric Unit (2, 18)

No.	Name	Count	Type	Full Name
1	K	14	Ligand/Ion	POTASSIUM ION
2	NA	4	Ligand/Ion	SODIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	K	-1	Ligand/Ion	POTASSIUM ION
2	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	K	-1	Ligand/Ion	POTASSIUM ION
2	NA	-1	Ligand/Ion	SODIUM ION

Sites (17, 17)

Asymmetric Unit (17, 17)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	DG A:4 , DG A:5 , DG B:14 , DG B:15 , DG C:24 , DG C:25 , DG D:34 , DG D:35 , K D:101	BINDING SITE FOR RESIDUE K A 101
02	AC2	SOFTWARE	DG A:2 , DG A:3 , K A:103 , DG B:12 , DG B:13 , DG C:22 , DG C:23 , DG D:32 , DG D:33 , K D:101	BINDING SITE FOR RESIDUE K A 102
03	AC3	SOFTWARE	DG A:2 , K A:102 , DG B:12 , DG C:22 , DG D:32 , DG E:42 , K E:101 , DG F:52 , DG G:62 , DG H:72	BINDING SITE FOR RESIDUE K A 103
04	AC4	SOFTWARE	DG A:3 , DG A:4 , K A:101 , K A:102 , DG B:13 , DG B:14 , DG C:23 , DG C:24 , DG D:33 , DG D:34	BINDING SITE FOR RESIDUE K D 101
05	AC5	SOFTWARE	K A:103 , DG E:42 , DG E:43 , DG F:52 , DG F:53 , K F:101 , DG G:62 , DG G:63 , DG H:72 , DG H:73	BINDING SITE FOR RESIDUE K E 101
06	AC6	SOFTWARE	DG E:44 , DG E:45 , DG F:54 , DG F:55 , K F:101 , DG G:64 , DG G:65 , DG H:74 , DG H:75	BINDING SITE FOR RESIDUE K E 102
07	AC7	SOFTWARE	DG E:43 , DG E:44 , K E:101 , K E:102 , DG F:53 , DG F:54 , DG G:63 , DG G:64 , DG H:73 , DG H:74	BINDING SITE FOR RESIDUE K F 101
08	AC8	SOFTWARE	DG I:2 , DG I:3 , DG J:12 , DG J:13 , K J:102 , DG K:22 , DG K:23 , DG L:32 , DG L:33 , K P:101	BINDING SITE FOR RESIDUE K I 101
09	AC9	SOFTWARE	DG I:4 , DG I:5 , DG J:14 , DG J:15 , K J:102 , DG K:24 , DG K:25 , DG L:34 , DG L:35	BINDING SITE FOR RESIDUE K J 101
10	BC1	SOFTWARE	DG I:3 , DG I:4 , K I:101 , DG J:13 , DG J:14 , K J:101 , DG K:23 , DG K:24 , DG L:33 , DG L:34	BINDING SITE FOR RESIDUE K J 102
11	BC2	SOFTWARE	DG M:43 , DG M:44 , K M:102 , DG N:53 , DG N:54 , K N:101 , DG O:63 , DG O:64 , DG P:73 , DG P:74	BINDING SITE FOR RESIDUE K M 101
12	BC3	SOFTWARE	DG M:44 , DG M:45 , K M:101 , DG N:54 , DG N:55 , DG O:64 , DG O:65 , DG P:74 , DG P:75	BINDING SITE FOR RESIDUE K M 102
13	BC4	SOFTWARE	DG M:42 , DG M:43 , K M:101 , DG N:52 , DG N:53 , DG O:62 , DG O:63 , DG P:72 , DG P:73 , K P:101	BINDING SITE FOR RESIDUE K N 101
14	BC5	SOFTWARE	DG N:53	BINDING SITE FOR RESIDUE NA N 102
15	BC6	SOFTWARE	DG O:63	BINDING SITE FOR RESIDUE NA O 101
16	BC7	SOFTWARE	DG I:2 , K I:101 , DG J:12 , DG K:22 , DG L:32 , DG M:42 , DG N:52 , K N:101 , DG O:62 , DG P:72	BINDING SITE FOR RESIDUE K P 101
17	BC8	SOFTWARE	DG P:73	BINDING SITE FOR RESIDUE NA P 102

SS Bonds (0, 0)

(no "SS Bond" information available for 4R44)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 4R44)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 4R44)

PROSITE Motifs (0, 0)

(no "PROSITE Motif" information available for 4R44)

Exons (0, 0)

(no "Exon" information available for 4R44)

Sequences/Alignments

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:DNA  Length:6
                                     
                  4r44 A  1 TGGGGT  6

Chain B from PDB  Type:DNA  Length:6
                                     
                  4r44 B 11 TGGGGT 16

Chain C from PDB  Type:DNA  Length:6
                                     
                  4r44 C 21 TGGGGT 26

Chain D from PDB  Type:DNA  Length:6
                                     
                  4r44 D 31 TGGGGT 36

Chain E from PDB  Type:DNA  Length:6
                                     
                  4r44 E 41 TGGGGT 46

Chain F from PDB  Type:DNA  Length:6
                                     
                  4r44 F 51 TGGGGT 56

Chain G from PDB  Type:DNA  Length:6
                                     
                  4r44 G 61 TGGGGT 66

Chain H from PDB  Type:DNA  Length:6
                                     
                  4r44 H 71 TGGGGT 76

Chain I from PDB  Type:DNA  Length:5
                                    
                  4r44 I  1 TGGGG  5

Chain J from PDB  Type:DNA  Length:5
                                    
                  4r44 J 11 TGGGG 15

Chain K from PDB  Type:DNA  Length:6
                                     
                  4r44 K 21 TGGGGT 26

Chain L from PDB  Type:DNA  Length:6
                                     
                  4r44 L 31 TGGGGT 36

Chain M from PDB  Type:DNA  Length:6
                                     
                  4r44 M 41 TGGGGT 46

Chain N from PDB  Type:DNA  Length:6
                                     
                  4r44 N 51 TGGGGT 56

Chain O from PDB  Type:DNA  Length:6
                                     
                  4r44 O 61 TGGGGT 66

Chain P from PDB  Type:DNA  Length:6
                                     
                  4r44 P 71 TGGGGT 76

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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

(no "SCOP Domain" information available for 4R44)

CATH Domains (0, 0)

(no "CATH Domain" information available for 4R44)

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 4R44)

Gene Ontology (0, 0)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 4R44)

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	Ligands, Modified Residues, Ions
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Related Entries

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Related Entries Specified in the PDB File

4r45	RACEMIC CRYSTAL STRUCTURE OF A BIMOLECULAR DNA G-QUADRUPLEX (P-1)
4r47	RACEMIC CRYSTAL STRUCTURE OF A BIMOLECULAR DNA G-QUADRUPLEX (P21/N)
4r48	RACEMIC CRYSTAL STRUCTURE OF A CALCIUM-BOUND DNA FOUR-WAY JUNCTION
4r49	RACEMIC CRYSTAL STRUCTURE OF A CALCIUM-BOUND B-DNA DUPLEX
4r4a	RACEMIC CRYSTAL STRUCTURE OF A COBALT-BOUND B-DNA DUPLEX
4r4d	RACEMIC CRYSTAL STRUCTURE OF A MAGNESIUM-BOUND B-DNA DUPLEX