5TB5 - JenaLib

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Title :   CRYSTAL STRUCTURE OF FULL-LENGTH FARNESYLATED AND METHYLATED KRAS4B IN COMPLEX WITH PDE-DELTA (CRYSTAL FORM I - WITH PARTIALLY DISORDERED HYPERVARIABLE REGION)

Authors :   S. Dharmaiah, T. H. Tran, D. K. Simanshu

Date :   11 Sep 16 (Deposition) - 02 Nov 16 (Release) - 16 Nov 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Kras4B, Pdedelta, Pde6Delta, Ras, Kras, Oncoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Dharmaiah, L. Bindu, T. H. Tran, W. K. Gillette, P. H. Frank, R. Ghirlando, D. V. Nissley, D. Esposito, F. Mccormick, A. G. Stephen, D. K. Simanshu
Structural Basis Of Recognition Of Farnesylated And Methylated Kras4B By Pde Delta.
Proc. Natl. Acad. Sci. Usa V. 113 E6766 2016
PubMed-ID: 27791178 | Reference-DOI: 10.1073/PNAS.1615316113

Molecule 1 - GTPASE KRAS
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	UNIDENTIFIED BACULOVIRUS
	Expression System Taxid	:	10469
	Gene	:	KRAS, KRAS2, RASK2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	K-RAS 2,KI-RAS,C-K-RAS,C-KI-RAS

Molecule 2 - RETINAL ROD RHODOPSIN-SENSITIVE CGMP 3',5'-CYCLIC PHOSPHODIESTERASE SUBUNIT DELTA
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	PDE6D, PDED
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	GMP-PDE DELTA,PROTEIN P17

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 8)

No.	Name	Count	Type	Full Name
1	CMT	2	Mod. Amino Acid	O-METHYLCYSTEINE
2	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
3	FAR	2	Ligand/Ion	FARNESYL
4	GDP	2	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE

Biological Unit 1 (4, 4)

No.	Name	Count	Type	Full Name
1	CMT	1	Mod. Amino Acid	O-METHYLCYSTEINE
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
3	FAR	1	Ligand/Ion	FARNESYL
4	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE

Biological Unit 2 (4, 4)

No.	Name	Count	Type	Full Name
1	CMT	1	Mod. Amino Acid	O-METHYLCYSTEINE
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
3	FAR	1	Ligand/Ion	FARNESYL
4	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:184 , CMT A:185 , SER B:39 , LEU B:63 , GLN B:78 , THR B:131 , PHE B:133	binding site for residue FAR A 201
2	AC2	SOFTWARE	GLY A:13 , VAL A:14 , GLY A:15 , LYS A:16 , SER A:17 , ALA A:18 , PHE A:28 , ASN A:116 , LYS A:117 , ASP A:119 , LEU A:120 , SER A:145 , ALA A:146 , LYS A:147 , HOH A:319 , HOH A:345 , HOH A:348	binding site for residue GDP A 202
3	AC3	SOFTWARE	ARG B:61 , LEU B:63 , PHE B:92 , TRP B:105 , SER B:107	binding site for residue EDO B 201
4	AC4	SOFTWARE	LYS C:184 , CMT C:185 , MET D:20 , LEU D:22 , SER D:39 , LEU D:76 , GLN D:78 , THR D:131 , PHE D:133	binding site for residue FAR C 201
5	AC5	SOFTWARE	ALA C:11 , GLY C:13 , VAL C:14 , GLY C:15 , LYS C:16 , SER C:17 , ALA C:18 , PHE C:28 , ASP C:30 , ALA C:59 , ASN C:116 , LYS C:117 , ASP C:119 , LEU C:120 , SER C:145 , ALA C:146 , LYS C:147 , HOH C:303	binding site for residue GDP C 202
6	AC6	SOFTWARE	ARG D:61 , LEU D:63 , PHE D:92 , TRP D:105 , SER D:107	binding site for residue EDO D 201

(no "SS Bond" information available for 5TB5)

(no "Cis Peptide Bond" information available for 5TB5)

(no "SAP(SNP)/Variant" information available for 5TB5)

(no "PROSITE Motif" information available for 5TB5)

(no "Exon" information available for 5TB5)

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:PROTEIN  Length:173
                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhhh....eeeeeee..eeeeeeeee......hhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeee.........hhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tb5 A   1 GTEYKLVVVGAGGVGKSALTIQLIQNHFDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEKMSKDKKKKSKTKc 185
                                    10        20       |39        49        59        69        79        89        99       109       119       129       139       149       159       169   ||  182  |
                                                      28|                                                                                                                                    173|     185-CMT
                                                       38                                                                                                                                     177

Chain B from PDB  Type:PROTEIN  Length:150
                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhheeeeeeeeee.....eeee..........eeeeeee.hhhhh.eeeeeeeeee...eeeeeeeeeeee..eeeeeeeeeeeee...eeeeeeeeee..hhhhh.hhhhhh..eeeeeeeee..eeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5tb5 B   1 MSAKDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSTEQMEKFRLEQKVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV 150
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain C from PDB  Type:PROTEIN  Length:172
                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhh.....eeeeeee....eeeeeeee..hhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeee.........hhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tb5 C   2 TEYKLVVVGAGGVGKSALTIQLIQNHFVDDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEKMSKKKKSKTKc 185
                                    11        21        38        48        58        68        78        88        98       108       118       128       138       148       158       168  ||   183 |
                                                       30|                                                                                                                                  171|     185-CMT
                                                        38                                                                                                                                   177

Chain D from PDB  Type:PROTEIN  Length:146
                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhheeeeeeeeee.....eeee..........eeeeeee.hhhhh.eeeeeeeeee...eeeeeeeeeeee..eeeeeeeeeeeee...eeeeeeeeee..hhhhh.hhhhhh..eeeeeeeee..eeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tb5 D   5 DERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSTEQMEKFRLEQKVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV 150
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144

Legend:		→ Mismatch	(orange background)
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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 5TB5)

(no "CATH Domain" information available for 5TB5)

(no "Pfam Domain" information available for 5TB5)

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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5tb5)

Biological Units
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		Biological Unit 2	[ Jena3D ]

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Description

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Ligands, Modified Residues, Ions (4, 8)

Sites (6, 6)

SS Bonds (0, 0)

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