4XZ3 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CA. KORARCHAEUM CRYPTOFILUM DINUCLEOTIDE FORMING ACETYL-COENZYME A SYNTHETASE 1 (SE-MET DERIVATIVE) IN COMPLEX WITH COENZYME A AND MG-AMPPCP, PHOSPHOHISTIDINE SEGMENT POINTING TOWARDS NUCLEOTIDE BINDING SITE

Authors :   R. H. -J. Weisse, A. J. Scheidig

Date :   03 Feb 15 (Deposition) - 27 Jan 16 (Release) - 10 Feb 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Dinucleotide Forming Acetyl-Coa Synthetase, Complex, Acd, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. H. Weie, A. Faust, M. Schmidt, P. Schonheit, A. J. Scheidig
Structure Of Ndp-Forming Acetyl-Coa Synthetase Acd1 Reveals A Large Rearrangement For Phosphoryl Transfer.
Proc. Natl. Acad. Sci. Usa V. 113 E519 2016
PubMed-ID: 26787904 | Reference-DOI: 10.1073/PNAS.1518614113

Molecule 1 - ACYL-COA SYNTHETASE (NDP FORMING)
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET17B
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	KCR_0198
	Organism Scientific	:	CANDIDATUS KORARCHAEUM CRYPTOFILUM OPF8
	Organism Taxid	:	374847

Molecule 2 - UNCHARACTERIZED PROTEIN
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET17B
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	KCR_0115
	Organism Scientific	:	CANDIDATUS KORARCHAEUM CRYPTOFILUM OPF8
	Organism Taxid	:	374847

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 41)

No.	Name	Count	Type	Full Name
1	ACP	4	Ligand/Ion	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2	COA	2	Ligand/Ion	COENZYME A
3	MG	5	Ligand/Ion	MAGNESIUM ION
4	MSE	30	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	VAL A:16 , GLY A:17 , SER A:19 , LYS A:24 , ILE A:25 , ASN A:46 , PRO A:47 , SER A:74 , VAL A:75 , PRO A:76 , LYS A:79 , VAL A:83 , ILE A:98 , THR A:99 , SER A:100 , ASN A:129 , ILE A:130 , PHE A:144 , GLY A:161	binding site for residue COA A 501
02	AC2	SOFTWARE	GLY A:307 , GLY A:308 , GLY A:309 , PHE A:343 , ALA A:344 , SER A:345 , MG A:503 , ASN C:129 , SER C:160 , GLY C:161 , ALA C:162	binding site for residue ACP A 502
03	AC3	SOFTWARE	ACP A:502	binding site for residue MG A 503
04	AC4	SOFTWARE	LYS B:60 , GLN B:111 , GLU B:112 , PHE B:113 , ALA B:114 , VAL B:223 , ASP B:224 , ARG B:226 , MG B:301 , HOH B:402 , HOH B:405 , HOH B:410	binding site for residue ACP B 300
05	AC5	SOFTWARE	ASP B:224 , ACP B:300 , HOH B:411	binding site for residue MG B 301
06	AC6	SOFTWARE	GLU A:104 , ASN A:129 , SER A:160 , GLY A:161 , ALA A:162 , GLY C:308 , GLY C:309 , PHE C:343 , SER C:345 , MG C:502	binding site for residue ACP C 501
07	AC7	SOFTWARE	ASP C:351 , ACP C:501	binding site for residue MG C 502
08	AC8	SOFTWARE	ASP C:66	binding site for residue MG C 503
09	AC9	SOFTWARE	VAL C:16 , GLY C:17 , SER C:19 , LYS C:24 , ILE C:25 , ASN C:46 , PRO C:47 , SER C:74 , VAL C:75 , PRO C:76 , LYS C:79 , VAL C:83 , ILE C:98 , SER C:100 , ASN C:129 , ILE C:130 , GLY C:161	binding site for residue COA C 504
10	AD1	SOFTWARE	SER D:70 , GLN D:111 , GLU D:112 , ALA D:114 , VAL D:223 , ASP D:224 , ARG D:226 , MG D:301	binding site for residue ACP D 300
11	AD2	SOFTWARE	ASN D:211 , ASP D:224 , ACP D:300	binding site for residue MG D 301

(no "SS Bond" information available for 4XZ3)

Asymmetric/Biological Unit

No.	Residues
1	Gly A:127	-	Pro A:128
2	Asn A:348	-	Pro A:349
3	Phe B:55	-	Pro B:56
4	Ala B:154	-	Pro B:155
5	Asn B:211	-	Pro B:212
6	Gly C:127	-	Pro C:128
7	Asn C:348	-	Pro C:349
8	Phe D:55	-	Pro D:56
9	Ala D:154	-	Pro D:155
10	Asn D:211	-	Pro D:212

(no "SAP(SNP)/Variant" information available for 4XZ3)

(no "PROSITE Motif" information available for 4XZ3)

(no "Exon" information available for 4XZ3)

Asymmetric/Biological 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:463
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh..eeeee.......hhhhhhhhhhhhhh...eeeee.....ee..ee...hhhhh.....eeee.....hhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhhhhhh..eee.....eeee.hhheeee.......eeeeeeee..hhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhh....eeeeee......hhhhhhhhhhhhhh...eeeee............hhhhhhhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhh.......eeeee.hhhhhhhhhhhhhhh.......hhhhhhhhh............ee.....hhhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhh...ee.hhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xz3 A   2 NDLERLFNPSAIAVVGASKDPSKIGSQILRNLLSYGFKGKVYPINPTADELmGLKCYPKVSDVPDKVDVAVISVPSDKVLGVIDDCGKAGVKFAVVITSGFKEVGNEELEEELVRRAHSYGmRVLGPNIFGYLYAPARLNATFGPKDVLSGNVAFISQSGALGIALmGYTVVENIGISSIVSVGNKADLDDVDLLDFFDKDPNTGVImIYLEGIAPGRGRmFIDVASRVSLRKPIIVIKAGRTEVGARAAASHTGSIAGSVAIYESAFKQSGILmAKSVEDAFDWTKALSWNPIPEGERLIVLTNGGGAGVQSTDTFADNGIYLSKPPESLIQEIKKFVPPFASFANPIDITGmAPDDWYYmGTLAALKNPDVDALTVLYCQTAVTTPIGVAKGIVDAIKEAGNSKPVTVGmVGGPEVAEAVSFLNKQRIAAYPTPERASSAmSALYAYARARSYVmKSLAVR 464
                                    11        21        31        41        51 |      61        71        81        91       101       111       121 |     131       141       151       161      |171       181       191       201       211       221|      231       241       251       261       271    |  281       291       301       311       321       331       341       351   |   361 |     371       381       391       401       411 |     421       431       441  |    451      |461   
                                                                              53-MSE                                                               123-MSE                                      168-MSE                                  209-MSE      222-MSE                                               276-MSE                                                                        355-MSE 363-MSE                                           413-MSE                        444-MSE       458-MSE

Chain B from PDB  Type:PROTEIN  Length:228
                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhh.....hhhhhhhhhhh.......eeee.hhhhhhhhhhhhh..eeeeee......hhhhh.eeeee.hhhhhhhhhhhhhhhhhhhh......eeeeee.....eeeeeeeeee...eeeeeeee...hhhhhh.eeeee...hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eee..eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4xz3 B   3 SRDLLLKAKENGRKSLLEHEAKYFISSYGIPVTNIRLAKSEEEAVNFSREIGFPVVLKIVSPQVVHKSDVGGVKVNLRSEEEVRKAYREIIENVKRNVPNAEIEGILVQEFAPPGVELIIGLLRDPQFGPTVmFGLGGVFVELFRDVSFRVAPLSEQDAESmIKEVKAYKLLTGFRGmEPVDIEAIKDALIRAGRIGVENEEIAEmDLNPVIAYPKGIKVVDARIILR 230
                                    12        22        32        42        52        62        72        82        92       102       112       122       132  |    142       152       162 |     172       182       192       202     | 212       222        
                                                                                                                                                              135-MSE                      164-MSE         180-MSE                     208-MSE

Chain C from PDB  Type:PROTEIN  Length:461
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh..eeeee.......hhhhhhhhhhhhhh...eeeee.....ee..ee...hhhhh.....eeee..hhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhhhhhh..eee.....eeee.hhheeee.......eeeeeeee.hhhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhh....eeeeee......hhhhhhhhhhhhhh...eeeee............hhhhhhhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhh.......eeeee.hhhhhhhhhhhhhhh.......hhhhhhhhhh...........ee.....hhhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xz3 C   3 DLERLFNPSAIAVVGASKDPSKIGSQILRNLLSYGFKGKVYPINPTADELmGLKCYPKVSDVPDKVDVAVISVPSDKVLGVIDDCGKAGVKFAVVITSGFKEVGNEELEEELVRRAHSYGmRVLGPNIFGYLYAPARLNATFGPKDVLSGNVAFISQSGALGIALmGYTVVENIGISSIVSVGNKADLDDVDLLDFFDKDPNTGVImIYLEGIAPGRGRmFIDVASRVSLRKPIIVIKAGRTEVGARAAASHTGSIAGSVAIYESAFKQSGILmAKSVEDAFDWTKALSWNPIPEGERLIVLTNGGGAGVQSTDTFADNGIYLSKPPESLIQEIKKFVPPFASFANPIDITGmAPDDWYYmGTLAALKNPDVDALTVLYCQTAVTTPIGVAKGIVDAIKEAGNSKPVTVGmVGGPEVAEAVSFLNKQRIAAYPTPERASSAmSALYAYARARSYVmKSLAV 463
                                    12        22        32        42        52|       62        72        82        92       102       112       122|      132       142       152       162     | 172       182       192       202      |212       222       232       242       252       262       272   |   282       292       302       312       322       332       342       352  |    362|      372       382       392       402       412|      422       432       442 |     452     | 462 
                                                                             53-MSE                                                               123-MSE                                      168-MSE                                  209-MSE      222-MSE                                               276-MSE                                                                        355-MSE 363-MSE                                           413-MSE                        444-MSE       458-MSE

Chain D from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.....hhhhhhhhhhh.......ee..hhhhhhhhhh..eeee.......hhhhhh.eeeee.hhhhhhhhhhhhhhh..eee.....eeeeeeeeee...eeeeeeee...hhhhhh.eeeee...hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eee..eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xz3 D   2 SSRDLLLKAKENGRKSLLEHEAKYFISSYGIPVTNIRLEEAVNFSREIGFPVVLKIVSPQVVHKSDVGGVKVNLRSEEEVRKAYREIIENILVQEFAPPGVELIIGLLRDPQFGPTVmFGLGGVFVELFRDVSFRVAPLSEQDAESmIKEVKAYKLLTGFRGmEPVDIEAIKDALIRAGRIGVENEEIAEmDLNPVIAYPKGIKVVDARIILR 230
                                    11        21        31       |45        55        65        75        85        95|      117       127       137       147       157      |167       177  |    187       197       207|      217       227   
                                                                39|                                                 95|                        135-MSE                      164-MSE         180-MSE                     208-MSE                  
                                                                 44                                                 108

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 4XZ3)

(no "CATH Domain" information available for 4XZ3)

(no "Pfam Domain" information available for 4XZ3)

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Ala B:154 - Pro B:155	[ RasMol ]
		Ala D:154 - Pro D:155	[ RasMol ]
		Asn A:348 - Pro A:349	[ RasMol ]
		Asn B:211 - Pro B:212	[ RasMol ]
		Asn C:348 - Pro C:349	[ RasMol ]
		Asn D:211 - Pro D:212	[ RasMol ]
		Gly A:127 - Pro A:128	[ RasMol ]
		Gly C:127 - Pro C:128	[ RasMol ]
		Phe B:55 - Pro B:56	[ RasMol ]
		Phe D:55 - Pro D:56	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 41)

Sites (11, 11)

SS Bonds (0, 0)

Cis Peptide Bonds (10, 10)

Sequence-Structure Mapping

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