5V9H - JenaLib

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Title :   STRUCTURE OF THE H477R VARIANT OF RAT CYTOSOLIC PEPCK IN COMPLEX WITH PHOSPHOGLYCOLATE AND GDP.

Authors :   T. Holyoak, D. S. Cui

Date :   23 Mar 17 (Deposition) - 12 Apr 17 (Release) - 26 Apr 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

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

Keywords :   Phosphoenolpyruvate Carboxykinase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. S. Cui, A. Broom, M. J. Mcleod, E. M. Meiering, T. Holyoak
Asymmetric Anchoring Is Required For Efficient Omega-Loop Opening And Closing In Cytosolic Phosphoenolpyruvate Carboxykinase.
Biochemistry V. 56 2106 2017
PubMed-ID: 28345895 | Reference-DOI: 10.1021/ACS.BIOCHEM.7B00178

Molecule 1 - PHOSPHOENOLPYRUVATE CARBOXYKINASE, CYTOSOLIC [GTP]
	Chains	:	A, B
	EC Number	:	4.1.1.32
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	PCK1
	Mutation	:	YES
	Organism Common	:	RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	PEPCK-C

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 13)

No.	Name	Count	Type	Full Name
1	1PE	1	Ligand/Ion	PENTAETHYLENE GLYCOL
2	GDP	2	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
3	MN	6	Ligand/Ion	MANGANESE (II) ION
4	NA	2	Ligand/Ion	SODIUM ION
5	PGA	2	Ligand/Ion	2-PHOSPHOGLYCOLIC ACID

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	1PE	1	Ligand/Ion	PENTAETHYLENE GLYCOL
2	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
3	MN	-1	Ligand/Ion	MANGANESE (II) ION
4	NA	-1	Ligand/Ion	SODIUM ION
5	PGA	1	Ligand/Ion	2-PHOSPHOGLYCOLIC ACID

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	1PE	-1	Ligand/Ion	PENTAETHYLENE GLYCOL
2	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
3	MN	-1	Ligand/Ion	MANGANESE (II) ION
4	NA	-1	Ligand/Ion	SODIUM ION
5	PGA	1	Ligand/Ion	2-PHOSPHOGLYCOLIC ACID

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LEU A:153 , TRP A:260 , LYS A:316 , ARG A:324 , GLU A:424 , HOH A:863	binding site for residue 1PE A 701
02	AC2	SOFTWARE	THR A:291 , GDP A:706 , PGA A:707 , HOH A:802 , HOH A:808 , HOH A:813	binding site for residue MN A 702
03	AC3	SOFTWARE	HIS A:502 , GLU A:607 , HOH A:872	binding site for residue MN A 703
04	AC4	SOFTWARE	LYS A:244 , HIS A:264 , ASP A:311 , PGA A:707	binding site for residue MN A 704
05	AC5	SOFTWARE	VAL A:65 , LEU A:79 , ASN A:208 , HOH A:847 , HOH A:860	binding site for residue NA A 705
06	AC6	SOFTWARE	PRO A:285 , ALA A:287 , CYS A:288 , GLY A:289 , LYS A:290 , THR A:291 , ASN A:292 , PRO A:337 , GLY A:338 , ARG A:436 , TRP A:516 , PHE A:517 , PHE A:525 , GLY A:529 , PHE A:530 , ASN A:533 , MN A:702 , PGA A:707 , HOH A:802 , HOH A:834 , HOH A:855 , HOH A:896	binding site for residue GDP A 706
07	AC7	SOFTWARE	ARG A:87 , LYS A:244 , HIS A:264 , SER A:286 , ALA A:287 , LYS A:290 , ASP A:311 , ARG A:405 , MN A:702 , MN A:704 , GDP A:706 , HOH A:808 , HOH A:813 , HOH A:814 , HOH A:835	binding site for residue PGA A 707
08	AC8	SOFTWARE	GLU B:63	binding site for residue MN B 701
09	AC9	SOFTWARE	THR B:291 , GDP B:705 , PGA B:706 , HOH B:803 , HOH B:812 , HOH B:846	binding site for residue MN B 702
10	AD1	SOFTWARE	LYS B:244 , HIS B:264 , ASP B:311 , PGA B:706	binding site for residue MN B 703
11	AD2	SOFTWARE	VAL B:65 , LEU B:79 , ASN B:208 , HOH B:827 , HOH B:884	binding site for residue NA B 704
12	AD3	SOFTWARE	PRO B:285 , ALA B:287 , CYS B:288 , GLY B:289 , LYS B:290 , THR B:291 , ASN B:292 , PRO B:337 , GLY B:338 , ARG B:436 , TRP B:516 , PHE B:517 , PHE B:525 , PHE B:530 , ASN B:533 , MN B:702 , PGA B:706 , HOH B:812 , HOH B:817 , HOH B:889 , HOH B:895 , HOH B:923	binding site for residue GDP B 705
13	AD4	SOFTWARE	ARG B:87 , LYS B:244 , HIS B:264 , SER B:286 , LYS B:290 , ASP B:311 , ARG B:405 , PHE B:485 , MN B:702 , MN B:703 , GDP B:705 , HOH B:802 , HOH B:803 , HOH B:812 , HOH B:846 , HOH B:869	binding site for residue PGA B 706

(no "SS Bond" information available for 5V9H)

Asymmetric Unit

No.	Residues
1	Leu A:200	-	Pro A:201
2	Leu B:200	-	Pro B:201

(no "SAP(SNP)/Variant" information available for 5V9H)

(no "PROSITE Motif" information available for 5V9H)

(no "Exon" information available for 5V9H)

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:611
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhh.eee......hhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh..eeee.....eeee.........hhh.eeee..hhhhhh............eehhhhhhhhhhh.........eeeeeeeee........eeeeeee.hhhhhhhhhhhheehhhhhhhhh....eeeeee.................hhhhheeeee....eeeee...hhhhhh..hhhhhhhhhhhhhhhhh.eee..eeeeee.....eeeeeee.....hhhhhhh........eeeeee...eeeee.....eeee....eeeee........hhhhhhhhh...eee..eee....ee.............ee.....ee.............eeeee................eeeeeeeee.........eee..hhhhhhhhhhhheee...........eee.hhhh......hhhhhhhhhhhh.........eeeee.........hhhhhhhhhhhhhhhhhh...eeee..eeee.............hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5v9h A   7 NGLDFSAKVIQGSLDSLPQEVRKFVEGNAQLCQPEYIHICDGSEEEYGRLLAHMQEEGVIRKLKKYDNCWLALTDPRDVARIESKTVIITQEQRDTVPIPKSGQSQLGRWMSEEDFEKAFNARFPGCMKGRTMYVIPFSMGPLGSPLAKIGIELTDSPYVVASMRIMTRMGTSVLEALGDGEFIKCLHSVGCPLPLKKPLVNNWACNPELTLIAHLPDRREIISFGSGYGGNSLLGKKCFALRIASRLAKEEGWLAEHMLILGITNPEGKKKYLAAAFPSACGKTNLAMMNPTLPGWKVECVGDDIAWMKFDAQGNLRAINPENGFFGVAPGTSVKTNPNAIKTIQKNTIFTNVAETSDGGVYWEGIDEPLAPGVTITSWKNKEWRPQDEEPCAHPNSRFCTPASQCPIIDPAWESPEGVPIEGIIFGGRRPAGVPLVYEALSWQHGVFVGAAMRSEATAAAEHKGKVIMRDPFAMRPFFGYNFGKYLAHWLSMAHRPAAKLPKIFHVNWFRKFLWPGFGENSRVLEWMFGRIEGEDSAKLTPIGYVPKEDALNLKGLGDVNVEELFGISKEFWEKEVEEIDKYLEDQVNADLPYEIERELRALKQRISQM 622
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516  ||   531       541       551       561       571       581       591       601       611       621 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          519|                                                                                                 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           525

Chain B from PDB  Type:PROTEIN  Length:609
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhh.eee......hhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh..eeee.....eeee.........hhh.eeee..hhhhhh............eehhhhhhhhhhh.........eeeeeeeee........eeeeeee.hhhhhhhhhhhheehhhhhhhhh....eeeeee......................eeeee....eeeee...hhhhhh..hhhhhhhhhhhhhhhhh.eee..eeeeee.....eeeeeee.....hhhhhhh........eeeeee...eeeee.....eeee....eeeee........hhhhhhhh....eee..eee...eee.............ee.....ee.............eeeee.hhh............eeeeeeeee.........eee..hhhhhhhhhhhheee...........eee.hhhh......hhhhhhhhhhhhhhh......eeeee.........hhhhhhhhhhhhhhhhhh...eeee..eeee.............hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5v9h B   9 LDFSAKVIQGSLDSLPQEVRKFVEGNAQLCQPEYIHICDGSEEEYGRLLAHMQEEGVIRKLKKYDNCWLALTDPRDVARIESKTVIITQEQRDTVPIPKSGQSQLGRWMSEEDFEKAFNARFPGCMKGRTMYVIPFSMGPLGSPLAKIGIELTDSPYVVASMRIMTRMGTSVLEALGDGEFIKCLHSVGCPLPLKKPLVNNWACNPELTLIAHLPDRREIISFGSGYGGNSLLGKKCFALRIASRLAKEEGWLAEHMLILGITNPEGKKKYLAAAFPSACGKTNLAMMNPTLPGWKVECVGDDIAWMKFDAQGNLRAINPENGFFGVAPGTSVKTNPNAIKTIQKNTIFTNVAETSDGGVYWEGIDEPLAPGVTITSWKNKEWRPQDEEPCAHPNSRFCTPASQCPIIDPAWESPEGVPIEGIIFGGRRPAGVPLVYEALSWQHGVFVGAAMRSEATAAAEHKGKVIMRDPFAMRPFFGYNFGKYLAHWLSMAHRPAAKLPKIFHVNWFRKFLWPGFGENSRVLEWMFGRIEGEDSAKLTPIGYVPKEDALNLKGLGDVNVEELFGISKEFWEKEVEEIDKYLEDQVNADLPYEIERELRALKQRISQM 622
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518||     533       543       553       563       573       583       593       603       613         
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        519|                                                                                                 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         525

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 5V9H)

(no "CATH Domain" information available for 5V9H)

(no "Pfam Domain" information available for 5V9H)

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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Leu A:200 - Pro A:201	[ RasMol ]
		Leu B:200 - Pro B:201	[ RasMol ]

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	5v9h
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	4.1.1.32
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5v95	SAME ENZYME VARIANT DIFFERENTLY LIGATED
5v97	SAME ENZYME VARIANT DIFFERENTLY LIGATED
5v9f	SAME ENZYME VARIANT DIFFERENTLY LIGATED
5v9g	SAME ENZYME VARIANT DIFFERENTLY LIGATED

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 13)

Sites (13, 13)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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Gene Ontology (42, 42)

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