4PHH - JenaLib

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Title :   CRYSTAL STRUCTURE OF YPT7 COVALENTLY MODIFIED WITH GNP

Authors :   D. Wiegandt, S. Vieweg, F. Hofmann, D. Koch, Y. Wu, A. Itzen, M. P. Muelle R. S. Goody

Date :   06 May 14 (Deposition) - 28 May 14 (Release) - 31 Aug 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.35

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

Keywords :   Ypt7, Acryl-Nucleotides, Agnp, Covalent, Gnp, Gppnhp, Endocytosis, Exocytosis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Wiegandt, S. Vieweg, F. Hofmann, D. Koch, F. Li, Y. W. Wu, A. Itzen, M. P. Muller, R. S. Goody
Locking Gtpases Covalently In Their Functional States.
Nat Commun V. 6 7773 2015
PubMed-ID: 26178622 | Reference-DOI: 10.1038/NCOMMS8773

Molecule 1 - GTP-BINDING PROTEIN YPT7
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 1-182
	Gene	:	YPT7, VAM4, YML001W, YM8270.02
	Mutation	:	YES
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	559292
	Strain	:	S288C

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 11)

No.	Name	Count	Type	Full Name
1	2UK	4	Ligand/Ion	5'-O-[(R)-HYDROXY{[(S)-HYDROXY(PHOSPHONOAMINO)PHOSPHORYL]OXY}PHOSPHORYL]-N-[3-(PROPANOYLAMINO)PROPYL]GUANOSINE
2	CL	3	Ligand/Ion	CHLORIDE ION
3	MG	4	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	2UK	1	Ligand/Ion	5'-O-[(R)-HYDROXY{[(S)-HYDROXY(PHOSPHONOAMINO)PHOSPHORYL]OXY}PHOSPHORYL]-N-[3-(PROPANOYLAMINO)PROPYL]GUANOSINE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	2UK	1	Ligand/Ion	5'-O-[(R)-HYDROXY{[(S)-HYDROXY(PHOSPHONOAMINO)PHOSPHORYL]OXY}PHOSPHORYL]-N-[3-(PROPANOYLAMINO)PROPYL]GUANOSINE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	2UK	1	Ligand/Ion	5'-O-[(R)-HYDROXY{[(S)-HYDROXY(PHOSPHONOAMINO)PHOSPHORYL]OXY}PHOSPHORYL]-N-[3-(PROPANOYLAMINO)PROPYL]GUANOSINE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	2UK	1	Ligand/Ion	5'-O-[(R)-HYDROXY{[(S)-HYDROXY(PHOSPHONOAMINO)PHOSPHORYL]OXY}PHOSPHORYL]-N-[3-(PROPANOYLAMINO)PROPYL]GUANOSINE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:16 , SER A:17 , GLY A:18 , VAL A:19 , GLY A:20 , LYS A:21 , THR A:22 , SER A:23 , TYR A:33 , SER A:34 , CYS A:35 , TYR A:37 , THR A:40 , GLY A:67 , ASN A:126 , LYS A:127 , ASP A:129 , SER A:158 , ALA A:159 , LYS A:160 , MG A:202 , HOH A:303 , HOH A:304 , HOH A:310	binding site for residue 2UK A 201
02	AC2	SOFTWARE	THR A:22 , THR A:40 , 2UK A:201 , HOH A:303 , HOH A:304	binding site for residue MG A 202
03	AC3	SOFTWARE	LYS A:101	binding site for residue CL A 203
04	AC4	SOFTWARE	THR B:22 , THR B:40 , ASP B:64 , 2UK B:201 , HOH B:301 , HOH B:302	binding site for residue MG B 202
05	AC5	SOFTWARE	ALA B:162 , VAL B:165 , ASP B:166 , LYS D:101	binding site for residue CL B 203
06	AC6	SOFTWARE	THR C:22 , THR C:40 , 2UK C:201 , HOH C:302 , HOH C:303	binding site for residue MG C 202
07	AC7	SOFTWARE	THR D:22 , THR D:40 , 2UK D:201 , HOH D:301 , HOH D:302	binding site for residue MG D 202
08	AC8	SOFTWARE	LYS B:101 , ALA D:162 , VAL D:165 , ASP D:166	binding site for residue CL D 203
09	AC9	SOFTWARE	SER B:17 , GLY B:18 , VAL B:19 , GLY B:20 , LYS B:21 , THR B:22 , SER B:23 , TYR B:33 , SER B:34 , THR B:40 , GLY B:67 , ASN B:126 , LYS B:127 , ASP B:129 , SER B:158 , ALA B:159 , LYS B:160 , MG B:202 , HOH B:301 , HOH B:302	binding site for Di-peptide 2UK B 201 and CYS B 35
10	AD1	SOFTWARE	SER C:17 , GLY C:18 , VAL C:19 , GLY C:20 , LYS C:21 , THR C:22 , SER C:23 , TYR C:33 , SER C:34 , GLN C:36 , TYR C:37 , THR C:40 , GLY C:67 , ASN C:126 , LYS C:127 , ASP C:129 , SER C:158 , ALA C:159 , LYS C:160 , MG C:202 , HOH C:302 , HOH C:303	binding site for Di-peptide 2UK C 201 and CYS C 35
11	AD2	SOFTWARE	GLU C:69 , ARG C:70 , SER D:17 , GLY D:18 , VAL D:19 , GLY D:20 , LYS D:21 , THR D:22 , SER D:23 , TYR D:33 , SER D:34 , LYS D:38 , ALA D:39 , THR D:40 , GLY D:67 , ASN D:126 , LYS D:127 , ASP D:129 , SER D:158 , ALA D:159 , LYS D:160 , MG D:202 , HOH D:301 , HOH D:302	binding site for Di-peptide 2UK D 201 and CYS D 35

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

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

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

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

(no "Exon" information available for 4PHH)

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:172
                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhh............eeeeeeee.....eeeeeeee...hhhhh.hhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhhh........eeeeee....hhhhh..hhhhhhhhhhhh....eeee......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4phh A   8 ILKVIILGDSGVGKTSLMHRYVNDKYSCQYKATIGADFLTKEVTVDGDKVATMQVWDTAGQERFQSVAFYRGADCCVLVYDVTNASSFENIKSWRDEFLVHANVNSPETFPFVILGNKIDAEESKKIVSEKSAQELAKSLGDIPLFLTSAKNAINVDTAFEEIARSALQQNQ 181
                                    17        27        37        47        57        67     || 79        89        99       109       119       129       139       149       159       169       179  
                                                                                            73|                                                                                                         
                                                                                             76

Chain B from PDB  Type:PROTEIN  Length:172
                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhh........eeeeeeeeee...eeeeeeeeee..hhhhh...hhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhhh........eeeeee....hhhhh..hhhhhhhhhhhh....eeee......hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4phh B   8 ILKVIILGDSGVGKTSLMHRYVNDKYSCATIGADFLTKEVTVDGDKVATMQVWDTAGQERFQSLGVAFYRGADCCVLVYDVTNASSFENIKSWRDEFLVHANVNSPETFPFVILGNKIDAEESKKIVSEKSAQELAKSLGDIPLFLTSAKNAINVDTAFEEIARSALQQNQA 182
                                    17        27       |40        50        60        70        80        90       100       110       120       130       140       150       160       170       180  
                                                      35|                                                                                                                                               
                                                       39

Chain C from PDB  Type:PROTEIN  Length:169
                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee....hhhhhhhhhhhh.............eeeee...eeeee............hhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhhh........eeeeee...........hhhhhhhhhhhh....eee.......hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4phh C   8 ILKVIILGDSGVGKTSLMHRYVNDKYSCQYKATIGADFLTKEVVATMQVWDTAGQERFQSLGVAFYRGADCCVLVYDVTNASSFENIKSWRDEFLVHANVNSPETFPFVILGNKIDAEESKKIVSEKSAQELAKSLGDIPLFLTSAKNAINVDTAFEEIARSALQQNQA 182
                                    17        27        37        47  ||    63        73        83        93       103       113       123       133       143       153       163       173         
                                                                     50|                                                                                                                             
                                                                      57

Chain D from PDB  Type:PROTEIN  Length:165
                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhh..........eeeeeee..eeeeeee.......hhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhhh........eeeeee...........hhhhhhhhhhhh....eee.......hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4phh D   7 NILKVIILGDSGVGKTSLMHRYVNDKYSCKATIGADFLTKEVTVATMQVWDTAGQERGVAFYRGADCCVLVYDVTNASSFENIKSWRDEFLVHANVNSPETFPFVILGNKIDAEESKKIVSEKSAQELAKSLGDIPLFLTSAKNAINVDTAFEEIARSALQQNQA 182
                                    16        26        38        48  ||    63      ||77        87        97       107       117       127       137       147       157       167       177     
                                                       35|           51|           70|                                                                                                           
                                                        38            57            75

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

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

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

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

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	YPT7_YEAST \| P32939	:	1ky2 1ky3 4phf 4phg

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 11)

Sites (11, 11)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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Gene Ontology (26, 26)

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