5KGN - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   1.95A RESOLUTION STRUCTURE OF INDEPENDENT PHOSPHOGLYCERATE MUTASE FROM C. ELEGANS IN COMPLEX WITH A MACROCYCLIC PEPTIDE INHIBITOR (2D)

Authors :   S. Lovell, N. Mehzabeen, K. P. Battaile, H. Yu, P. Dranchak, R. Macarthu T. Carlow, H. Suga, J. Inglese

Date :   13 Jun 16 (Deposition) - 05 Apr 17 (Release) - 26 Apr 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

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

Keywords :   Metal Binding, Coupled Enzyme Assay, Hts, Structure Activity Relationship, Rapid Systems, High Throughput Enzymology, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Yu, P. Dranchak, Z. Li, R. Macarthur, M. S. Munson, N. Mehzabeen, N. J. Baird, K. P. Battalie, D. Ross, S. Lovell, C. K. Carlow, H. Suga, J. Inglese
Macrocycle Peptides Delineate Locked-Open Inhibition Mechanism For Microorganism Phosphoglycerate Mutases.
Nat Commun V. 8 14932 2017
PubMed-ID: 28368002 | Reference-DOI: 10.1038/NCOMMS14932

Molecule 1 - 2,3-BISPHOSPHOGLYCERATE-INDEPENDENT PHOSPHOGLYCERATE MUTASE
	Chains	:	A, B
	EC Number	:	5.4.2.12
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21A(+)
	Expression System Strain	:	C2566/T7 EXPRESS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	ISOFORM B
	Gene	:	IPGM-1, F57B10.3
	Organism Scientific	:	CAENORHABDITIS ELEGANS
	Organism Taxid	:	6239
	Other Details	:	THIS FORM OF THE ENZYME (M19 TO I539, ISOFORM B) IS MISSING THE FIRST 18 RESIDUES RELATIVE TO THE FULL LENGTH SEQUENCE.
	Synonym	:	IPGM,COFACTOR-INDEPENDENT PHOSPHOGLYCERATE MUTASE HOMOLOG

Molecule 2 - MACROCYCLIC PEPTIDE INHIBITOR
	Chains	:	C, D
	Engineered	:	YES
	Organism Scientific	:	SYNTHETIC CONSTRUCT
	Organism Taxid	:	32630
	Other Details	:	THIS IS A SYNTHETICALLY PREPARED PEPTIDE INHIBITOR. D- TYROSINE CONNECTED TO THE SG ATOM OF CYS 8 BY A THIOETHER LINKAGE TO FORM THE MACROCYCLIC PEPTIDE.
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (8, 16)

No.	Name	Count	Type	Full Name
1	ACE	2	Mod. Amino Acid	ACETYL GROUP
2	CL	2	Ligand/Ion	CHLORIDE ION
3	DTY	2	Mod. Amino Acid	D-TYROSINE
4	GOL	2	Ligand/Ion	GLYCEROL
5	MG	2	Ligand/Ion	MAGNESIUM ION
6	MN	2	Ligand/Ion	MANGANESE (II) ION
7	NH2	2	Mod. Amino Acid	AMINO GROUP
8	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (4, 4)

No.	Name	Count	Type	Full Name
1	ACE	1	Mod. Amino Acid	ACETYL GROUP
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	DTY	1	Mod. Amino Acid	D-TYROSINE
4	GOL	1	Ligand/Ion	GLYCEROL
5	MG	-1	Ligand/Ion	MAGNESIUM ION
6	MN	-1	Ligand/Ion	MANGANESE (II) ION
7	NH2	1	Mod. Amino Acid	AMINO GROUP
8	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (4, 4)

No.	Name	Count	Type	Full Name
1	ACE	1	Mod. Amino Acid	ACETYL GROUP
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	DTY	1	Mod. Amino Acid	D-TYROSINE
4	GOL	1	Ligand/Ion	GLYCEROL
5	MG	-1	Ligand/Ion	MAGNESIUM ION
6	MN	-1	Ligand/Ion	MANGANESE (II) ION
7	NH2	1	Mod. Amino Acid	AMINO GROUP
8	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (18, 18)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:97 , ASN A:336 , HOH A:869	binding site for residue CL A 601
02	AC2	SOFTWARE	HIS A:147 , ARG A:177 , ASP A:178 , ARG A:210 , ARG A:216 , ARG A:284 , ARG A:287	binding site for residue GOL A 602
03	AC3	SOFTWARE	ILE A:50 , LEU A:51 , ALA A:53 , THR A:55 , HOH A:808 , HOH A:944	binding site for residue MG A 603
04	AC4	SOFTWARE	ASP A:426 , HIS A:430 , HIS A:485 , HOH A:770 , HOH A:998 , HOH A:1000	binding site for residue MN A 604
05	AC5	SOFTWARE	ASP A:37 , SER A:86 , ASP A:467 , HIS A:468	binding site for residue ZN A 605
06	AC6	SOFTWARE	ARG B:97 , ASN B:336	binding site for residue CL B 601
07	AC7	SOFTWARE	HIS B:147 , ARG B:177 , ASP B:178 , ARG B:210 , ARG B:216 , ARG B:284 , ARG B:287	binding site for residue GOL B 602
08	AC8	SOFTWARE	ILE B:50 , LEU B:51 , ALA B:53 , THR B:55 , HOH B:735 , HOH B:807	binding site for residue MG B 603
09	AC9	SOFTWARE	ASP B:426 , HIS B:430 , HIS B:485 , HOH B:711 , HOH B:933 , HOH B:952	binding site for residue MN B 604
10	AD1	SOFTWARE	ASP B:37 , SER B:86 , ASP B:467 , HIS B:468	binding site for residue ZN B 605
11	AD2	SOFTWARE	GLU A:87 , PHE A:365 , PHE A:366 , ASP C:2 , TYR C:3 , ASP C:6 , TYR C:7 , CYS C:8 , TYR C:9 , TYR C:11 , NH2 C:12 , HOH C:104 , HOH C:107	binding site for Di-peptide ACE C 0 and DTY C 1
12	AD3	SOFTWARE	DTY C:1 , ASP C:2 , ASP C:6 , TYR C:7 , TYR C:9 , LEU C:10 , TYR C:11 , NH2 C:12	binding site for Di-peptide ACE C 0 and CYS C 8
13	AD4	SOFTWARE	GLU A:87 , ARG A:289 , PHE A:365 , PHE A:366 , ACE C:0 , TYR C:3 , ASP C:6 , CYS C:8 , TYR C:9 , TYR C:11 , NH2 C:12 , HOH C:101 , HOH C:104 , HOH C:106 , HOH C:107	binding site for Di-peptide DTY C 1 and ASP C 2
14	AD5	SOFTWARE	ASN A:85 , GLU A:87 , DTY C:1 , CYS C:8 , TYR C:9 , LEU C:10	binding site for Di-peptide TYR C 11 and NH2 C 12
15	AD6	SOFTWARE	DTY D:1 , ASP D:2 , ASP D:6 , TYR D:7 , TYR D:9 , LEU D:10 , TYR D:11 , NH2 D:12	binding site for Di-peptide ACE D 0 and CYS D 8
16	AD7	SOFTWARE	GLU B:87 , PHE B:365 , PHE B:366 , ASP D:2 , TYR D:3 , ASP D:6 , TYR D:7 , CYS D:8 , TYR D:9 , NH2 D:12 , HOH D:103 , HOH D:105	binding site for Di-peptide ACE D 0 and DTY D 1
17	AD8	SOFTWARE	GLU B:87 , ARG B:289 , PHE B:365 , PHE B:366 , ACE D:0 , TYR D:3 , ASP D:6 , CYS D:8 , TYR D:9 , NH2 D:12 , HOH D:101 , HOH D:103 , HOH D:105 , HOH D:106	binding site for Di-peptide DTY D 1 and ASP D 2
18	AD9	SOFTWARE	ASN B:85 , GLU B:87 , HOH B:727 , DTY D:1 , CYS D:8 , TYR D:9 , LEU D:10	binding site for Di-peptide TYR D 11 and NH2 D 12

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

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

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

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

(no "Exon" information available for 5KGN)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	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:530
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh..eeeeeee...........hhhhhh.hhhhhhhh...eeee..hhhhhh.......hhhhhhhhhhhh....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..eeeeeee........hhhhhhhhhhhhhhh...eeeeeeee........hhhhhhhhhhhhhhhh....eeeeeeehhhhh....hhhhhhhhhhhhhhh..ee....hhhhhhhhhhhh..hhhhh..ee.hhhhhh.....eeee.......hhhhhhhhhh.hhhhhh.........eeee..........ee.........hhhhhhhhh...eeeeee..hhhhhh.............eeeeee......hhhhh...hhhhhhhhhhhhhhhh...eeeeeehhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeee.......................eeee.....eee........hhhhhhhhhhhhhh............eeehhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kgn A  20 AMANNSSVANKVCLIVIDGWGVSEDPYGNAILNAQTPVMDKLCSGNWAQIEAHGLHVGLPEGLMGNSEVGHLNIGAGRVIYQDIVRINLAVKNNKFVTNESLVDACDRAKNGNGRLHLAGLVSDGGVHSHIDHMFALVKAIKELGVPELYLHFYGDGRDTSPNSGVGFLEQTLEFLEKTTGYGKLATVVGRYYAMDRDNRWERINVAYEAMIGGVGETSDEAGVVEVVRKRYAADETDEFLKPIILQGEKGRVQNDDTIIFFDYRADRMREISAAMGMDRYKDCNSKLAHPSNLQVYGMTQYKAEFPFKSLFPPASNKNVLAEWLAEQKVSQFHCAETEKYAHVTFFFNGGLEKQFEGEERCLVPSPKVATYDLQPEMSAAGVADKMIEQLEAGTHPFIMCNFAPPDMVGHTGVYEAAVKACEATDIAIGRIYEATQKHGYSLMVTADHGNAEKMKAPDGGKHTAHTCYRVPLTLSHPGFKFVDPADRHPALCDVAPTVLAIMGLPQPAEMTGVSIVQKIKLAAALEHHH 549
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549

Chain B from PDB  Type:PROTEIN  Length:521
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh..eeeeeee...........hhhhhh.hhhhhhhh...eeee..hhhhhh.......hhhhhhhhhhhh....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..eeeeeee........hhhhhhhhhhhhhhh...eeeeeeee........hhhhhhhhhhhhhhhh....eeeeeeehhhhh....hhhhhhhhhhhhhhh..ee....hhhhhhhhhhhh..hhhhh..ee.hhhhhh.....eeee.......hhhhhhhhhh.hhhhhh.........eeee..........ee.........hhhhhhhhh...eeeeee..hhhhhh.............eeeeee......hhhhh...hhhhhhhhhhhhhhhh...eeeeeehhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeee.......................eeee.....eee........hhhhhhhhhhhhhh............eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kgn B  19 MAMANNSSVANKVCLIVIDGWGVSEDPYGNAILNAQTPVMDKLCSGNWAQIEAHGLHVGLPEGLMGNSEVGHLNIGAGRVIYQDIVRINLAVKNNKFVTNESLVDACDRAKNGNGRLHLAGLVSDGGVHSHIDHMFALVKAIKELGVPELYLHFYGDGRDTSPNSGVGFLEQTLEFLEKTTGYGKLATVVGRYYAMDRDNRWERINVAYEAMIGGVGETSDEAGVVEVVRKRYAADETDEFLKPIILQGEKGRVQNDDTIIFFDYRADRMREISAAMGMDRYKDCNSKLAHPSNLQVYGMTQYKAEFPFKSLFPPASNKNVLAEWLAEQKVSQFHCAETEKYAHVTFFFNGGLEKQFEGEERCLVPSPKVATYDLQPEMSAAGVADKMIEQLEAGTHPFIMCNFAPPDMVGHTGVYEAAVKACEATDIAIGRIYEATQKHGYSLMVTADHGNAEKMKAPDGGKHTAHTCYRVPLTLSHPGFKFVDPADRHPALCDVAPTVLAIMGLPQPAEMTGVSIVQKI 539
                                    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       528       538

Chain C from PDB  Type:PROTEIN  Length:13
                                             
               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
                 5kgn C   0 xxDYPGDYCYLYx  12
                            ||       9  |
                            0-ACE      12-NH2
                             1-DTY

Chain D from PDB  Type:PROTEIN  Length:13
                                             
               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
                 5kgn D   0 xxDYPGDYCYLYx  12
                            ||       9  |
                            ||         12-NH2
                            0-ACE        
                             1-DTY

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 5KGN)

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

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

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (8, 16)

Sites (18, 18)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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