4UD7 - JenaLib

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Biological Unit 4 (Jmol Viewer)

Title :   STRUCTURE OF THE STAPLED PEPTIDE YS-02 BOUND TO MDM2

Authors :   Y. S. Tan, J. Reeks, C. J. Brown, C. E. Jennings, R. S. Eapen, Q. S. Tng, D. T Y. T. Ying, F. J. F. Gago, D. P. Lane, M. E. M. Noble, C. Verma

Date :   08 Dec 14 (Deposition) - 13 Jan 16 (Release) - 18 Jan 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

Chains :   Asym. Unit : A,B,C,D,F,G,H,I
Biol. Unit 1: C,H  (1x)
Biol. Unit 2: D,I  (1x)
Biol. Unit 3: B,G  (1x)
Biol. Unit 4: A,F  (1x)

Keywords :   Lyase, Mdm2, Stapled Peptide, P53 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. S. Tan, J. Reeks, C. J. Brown, D. Thean, F. J. Ferrer Gago, T. Y. Yuen, E. T. Goh, X. E. Lee, C. E. Jennings, T. L. Joseph, R. Lakshminarayanan, D. P. Lane, M. E. Noble, C. S. Verma
Benzene Probes In Molecular Dynamics Simulations Reveal Novel Binding Sites For Ligand Design.
J Phys Chem Lett V. 7 3452 2016
PubMed-ID: 27532490 | Reference-DOI: 10.1021/ACS.JPCLETT.6B01525

Molecule 1 - MDM2
	Chains	:	A, B, C, D
	EC Number	:	6.3.2.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX6P-1
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	PLYSS
	Expression System Vector Type	:	PLASMID
	Fragment	:	P53 BINDING DOMAIN, UNP RESIDUES 17-125
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 2 - YS-02
	Chains	:	F, G, H, I
	Engineered	:	YES
	Organism Scientific	:	SYNTHETIC CONSTRUCT
	Organism Taxid	:	32630
	Other Details	:	STAPLED PEPTIDE, COVALENT BOND BETWEEN THE SIDE CHAINS OF RESIDUES 20 AND 24.
	Synthetic	:	YES

		1	2	3	4	5	6	7	8
Asymmetric Unit	:	A	B	C	D	F	G	H	I
Biological Unit 1 (1x)	:			C				H
Biological Unit 2 (1x)	:				D				I
Biological Unit 3 (1x)	:		B				G
Biological Unit 4 (1x)	:	A				F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 12)

No.	Name	Count	Type	Full Name
1	2JN	8	Mod. Amino Acid	2-METHYL-D-NORLEUCINE
2	ACE	2	Mod. Amino Acid	ACETYL GROUP
3	NH2	2	Mod. Amino Acid	AMINO GROUP

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	2JN	2	Mod. Amino Acid	2-METHYL-D-NORLEUCINE
2	ACE	1	Mod. Amino Acid	ACETYL GROUP
3	NH2	-1	Mod. Amino Acid	AMINO GROUP

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	2JN	2	Mod. Amino Acid	2-METHYL-D-NORLEUCINE
2	ACE	-1	Mod. Amino Acid	ACETYL GROUP
3	NH2	-1	Mod. Amino Acid	AMINO GROUP

Biological Unit 3 (2, 3)

No.	Name	Count	Type	Full Name
1	2JN	2	Mod. Amino Acid	2-METHYL-D-NORLEUCINE
2	ACE	-1	Mod. Amino Acid	ACETYL GROUP
3	NH2	1	Mod. Amino Acid	AMINO GROUP

Biological Unit 4 (3, 4)

No.	Name	Count	Type	Full Name
1	2JN	2	Mod. Amino Acid	2-METHYL-D-NORLEUCINE
2	ACE	1	Mod. Amino Acid	ACETYL GROUP
3	NH2	1	Mod. Amino Acid	AMINO GROUP

(no "Site" information available for 4UD7)

(no "SS Bond" information available for 4UD7)

(no "Cis Peptide Bond" information available for 4UD7)

(no "SAP(SNP)/Variant" information available for 4UD7)

(no "PROSITE Motif" information available for 4UD7)

(no "Exon" information available for 4UD7)

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:97
                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhheee...hhhhhhhhhhh.......hhhhhhhhhhhhhhhh.........eee...hhhhhhhh..eee..hhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 4ud7 A  15 GSSQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDAAQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVN 111
                                    24        34        44        54        64        74        84        94       104

Chain B from PDB  Type:PROTEIN  Length:96
                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhheee...hhhhhhhhhh........hhhhhhhhhhhhhhhh.........eee...hhhhhhhh..eee..hhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 4ud7 B  16 SSQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDAAQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVN 111
                                    25        35        45        55        65        75        85        95       105

Chain C from PDB  Type:PROTEIN  Length:96
                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhh.eeeehhhhhhhhhhh......eehhhhhhhhhhhhhhh.........eee...hhhhhhhh..eee..hhhhhhhhhhh.eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 4ud7 C  17 SQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDAAQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVNQ 112
                                    26        36        46        56        66        76        86        96       106

Chain D from PDB  Type:PROTEIN  Length:96
                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhh.eeeehhhhhhhhhhhh.....eehhhhhhhhhhhhhhh.........eee..hhhhhhhhh..eee..hhhhhhhhhhhheee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 4ud7 D  17 SQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDAAQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVNQ 112
                                    26        36        46        56        66        76        86        96       106

Chain F from PDB  Type:PROTEIN  Length:16
                                                
               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
                 4ud7 F  16 xTSFxEYWxLLPENYx  31
                            |   |   25     |
                           16-ACE   |     31-NH2
                               20-2JN       
                                   24-2JN

Chain G from PDB  Type:PROTEIN  Length:15
                                               
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author ........hhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                 4ud7 G  17 TSFxEYWxLLPENYx  31
                               |   |26    |
                               |   |     31-NH2
                              20-2JN       
                                  24-2JN

Chain H from PDB  Type:PROTEIN  Length:12
                                            
               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
                 4ud7 H  16 xTSFxEYWxLLP  27
                            |   |   25  
                            |   |   |   
                           16-ACE   |   
                               20-2JN   
                                   24-2JN

Chain I from PDB  Type:PROTEIN  Length:10
                                          
               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
                 4ud7 I  17 TSFxEYWxLL  26
                               |   |26
                              20-2JN  
                                  24-2JN

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 4UD7)

(no "CATH Domain" information available for 4UD7)

(no "Pfam Domain" information available for 4UD7)

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	Sites
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Biological Units
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4ue1	STRUCTURE OF THE STAPLED PEPTIDE YS-01 BOUND TO MDM2

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 12)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (83, 83)

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