5FPP - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF A PRE-REACTION TERNARY COMPLEX BETWEEN SARIN-ACETYLCHOLINESTERASE AND HI-6

Authors :   A. Allgardsson, L. Berg, C. Akfur, A. Hornberg, F. Worek, A. Linusson, F

Date :   02 Dec 15 (Deposition) - 11 May 16 (Release) - 01 Jun 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Hydrolase, Sarin, Hi-6, Qm, Density Functional Theory Calculations, Michaelis Complex. (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Allgardsson, L. Berg, C. Akfur, A. Hornberg, F. Worek, A. Linusson, F. J. Ekstrom
Structure Of A Prereaction Complex Between The Nerve Agent Sarin, Its Biological Target Acetylcholinesterase, And The Antidote Hi-6.
Proc. Natl. Acad. Sci. Usa V. 113 5514 2016
PubMed-ID: 27140636 | Reference-DOI: 10.1073/PNAS.1523362113

Molecule 1 - ACETYLCHOLINESTERASE
	Chains	:	A, B
	EC Number	:	3.1.1.7
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK293F
	Expression System Common	:	HUMAN
	Expression System Taxid	:	9606
	Fragment	:	CATALYTIC DOMAIN, UNP RESIDUES 32-574
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	SARIN PHOSPHONYLATION PRODUCT COVALENTLY ATTACHED TO SER203
	Synonym	:	ACHE

		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 (6, 10)

No.	Name	Count	Type	Full Name
1	AE3	2	Ligand/Ion	2-(2-ETHOXYETHOXY)ETHANOL
2	CO3	2	Ligand/Ion	CARBONATE ION
3	HI6	2	Ligand/Ion	4-(AMINOCARBONYL)-1-[({2-[(E)-(HYDROXYIMINO)METHYL]PYRIDINIUM-1-YL}METHOXY)METHYL]PYRIDINIUM
4	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	P6G	1	Ligand/Ion	HEXAETHYLENE GLYCOL
6	SGB	2	Mod. Amino Acid	O-[(S)-METHYL(1-METHYLETHOXY)PHOSPHORYL]-L-SERINE

Biological Unit 1 (6, 6)

No.	Name	Count	Type	Full Name
1	AE3	1	Ligand/Ion	2-(2-ETHOXYETHOXY)ETHANOL
2	CO3	1	Ligand/Ion	CARBONATE ION
3	HI6	1	Ligand/Ion	4-(AMINOCARBONYL)-1-[({2-[(E)-(HYDROXYIMINO)METHYL]PYRIDINIUM-1-YL}METHOXY)METHYL]PYRIDINIUM
4	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	P6G	1	Ligand/Ion	HEXAETHYLENE GLYCOL
6	SGB	1	Mod. Amino Acid	O-[(S)-METHYL(1-METHYLETHOXY)PHOSPHORYL]-L-SERINE

Biological Unit 2 (4, 4)

No.	Name	Count	Type	Full Name
1	AE3	1	Ligand/Ion	2-(2-ETHOXYETHOXY)ETHANOL
2	CO3	1	Ligand/Ion	CARBONATE ION
3	HI6	1	Ligand/Ion	4-(AMINOCARBONYL)-1-[({2-[(E)-(HYDROXYIMINO)METHYL]PYRIDINIUM-1-YL}METHOXY)METHYL]PYRIDINIUM
4	NAG	-1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	P6G	-1	Ligand/Ion	HEXAETHYLENE GLYCOL
6	SGB	1	Mod. Amino Acid	O-[(S)-METHYL(1-METHYLETHOXY)PHOSPHORYL]-L-SERINE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:286	BINDING SITE FOR RESIDUE CO3 A1549
2	AC2	SOFTWARE	HIS A:381 , GLN A:527 , PHE A:535 , HOH A:2214 , HOH A:2263 , ALA B:377 , LEU B:380 , HIS B:381 , GLN B:527 , PHE B:535	BINDING SITE FOR RESIDUE P6G A1550
3	AC3	SOFTWARE	HIS A:393 , ASP A:404 , ARG A:525 , THR A:528	BINDING SITE FOR RESIDUE AE3 A1551
4	AC4	SOFTWARE	ASP A:74 , TYR A:124 , SGB A:203 , TRP A:286 , ARG A:296 , PHE A:297 , SER A:298 , TYR A:337 , PHE A:338 , TYR A:341	BINDING SITE FOR RESIDUE HI6 A1552
5	AC5	SOFTWARE	TRP B:86 , TYR B:124 , GLU B:202 , SGB B:203 , PHE B:295 , TYR B:337 , PHE B:338 , TYR B:341 , HOH B:2194	BINDING SITE FOR RESIDUE HI6 B1545
6	AC6	SOFTWARE	GLN A:527	BINDING SITE FOR RESIDUE AE3 B1546
7	AC7	SOFTWARE	TRP B:286 , HOH B:2123	BINDING SITE FOR RESIDUE CO3 B1547
8	AC8	SOFTWARE	SER A:347 , ASN A:350 , HOH A:2200 , HOH A:2202 , HOH A:2207	BINDING SITE FOR MONO-SACCHARIDE NAG A 601 BOUND TO ASN A 350

Asymmetric Unit

No.	Residues
1	A:69	-	A:96
2	A:257	-	A:272
3	A:409	-	A:529
4	B:69	-	B:96
5	B:257	-	B:272
6	B:409	-	B:529

Asymmetric Unit

No.	Residues
1	Tyr A:105	-	Pro A:106
2	Thr A:545	-	Glu A:546
3	Tyr B:105	-	Pro B:106
4	Ser B:497	-	Pro B:498

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

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

(no "Exon" information available for 5FPP)

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:541
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhh.eeee..eeee.eeeee..eeeeeeeeee.....hhhhh............eee......ee..........hhhhhh......ee....eeeeeee.......eeeeeee...........hhhhhhhhhhhhhh.eeeee...hhhhhhh..........hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeehhhhhhhhhhhhhhhhhh...eeeee...........hhhhhhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhhhhhhhh.....................hhhhhhhhh.....eeeeeee...hhhhhhhhh...........hhhhhhhhhhhhh...hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.........hhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.....................eeeee.....eeee..hhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fpp A   1 EGREDPQLLVRVRGGQLRGIRLKAPGGPVSAFLGIPFAEPPVGSRRFMPPEPKRPWSGVLDATTFQNVCYQYVDTLYPGFEGTEMWNPNRELSEDCLYLNVWTPYPRPASPTPVLIWIYGGGFYSGAASLDVYDGRFLAQVEGAVLVSMNYRVGTFGFLALPGSREAPGNVGLLDQRLALQWVQENIAAFGGDPMSVTLFGEsAGAASVGMHILSLPSRSLFHRAVLQSGTPNGPWATVSAGEARRRATLLARLVGCNDTELIACLRTRPAQDLVDHEWHVLPQESIFRFSFVPVVDGDFLSDTPEALINTGDFQDLQVLVGVVKDEGSYFLVYGVPGFSKDNESLISRAQFLAGVRIGVPQASDLAAEAVVLHYTDWLHPEDPTHLRDAMSAVVGDHNVVCPVAQLAGRLAAQGARVYAYIFEHRASTLTWPLWMGVPHGYEIEFIFGLPLDPSLNYTTEERIFAQRLMKYWTNFARTGDPNDPRDSKSPQWPPYTTAAQQYVSLNLKPLEVRRGLRAQTCAFWNRFLPKLLSATATEAP 548
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200  |    210       220       230       240       250      |267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547 
                                                                                                                                                                                                                                    203-SGB                                               257|                                                                                                                                                                                                                                                                                           
                                                                                                                                                                                                                                                                                           265

Chain B from PDB  Type:PROTEIN  Length:533
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhh.eeee..eeee.eeeee..eeeeeeeeee.....hhhhh............eee......ee..........hhhhhh......ee....eeeeeee.......eeeeeee...........hhhhhhhhhhhhhh.eeeee...hhhhhhh..........hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeehhhhhhhhhhhhhhhhhh...eeeee...........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh........................hhhhhhhhh.....eeeeeee...hhhhhhhhh...........hhhhhhhhhhhhh...hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.........hhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.....................eeeee.....eeee..hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fpp B   5 DPQLLVRVRGGQLRGIRLKAPGGPVSAFLGIPFAEPPVGSRRFMPPEPKRPWSGVLDATTFQNVCYQYVDTLYPGFEGTEMWNPNRELSEDCLYLNVWTPYPRPASPTPVLIWIYGGGFYSGAASLDVYDGRFLAQVEGAVLVSMNYRVGTFGFLALPGSREAPGNVGLLDQRLALQWVQENIAAFGGDPMSVTLFGEsAGAASVGMHILSLPSRSLFHRAVLQSGTPNGPWATVSAGEARRRATLLARLVGCNDTELIACLRTRPAQDLVDHEWHVLPQESIFRFSFVPVVDGDFLSDTPEALINTGDFQDLQVLVGVVKDEGSYFLVYGVPGFSKDNESLISRAQFLAGVRIGVPQASDLAAEAVVLHYTDWLHPEDPTHLRDAMSAVVGDHNVVCPVAQLAGRLAAQGARVYAYIFEHRASTLTWPLWMGVPHGYEIEFIFGLPLDPSLNYTTEERIFAQRLMKYWTNFARTGDPNDPRDSKSPQWPPYTTAAQQYVSLNLKPLEVRRGLRAQTCAFWNRFLPKLLSATA 544
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254  ||   271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541   
                                                                                                                                                                                                                                203-SGB                                               257|                                                                                                                                                                                                                                                                                       
                                                                                                                                                                                                                                                                                       265

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 5FPP)

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

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

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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Ser B:497 - Pro B:498	[ RasMol ]
		Thr A:545 - Glu A:546	[ RasMol ]
		Tyr A:105 - Pro A:106	[ RasMol ]
		Tyr B:105 - Pro B:106	[ RasMol ]

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	5fpp
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5foq	ACETYLCHOLINESTERASE IN COMPLEX WITH C7653
5fpq	STRUCTURE OF HOMO SAPIENS ACETYLCHOLINESTERASE PHOSPHONYLATED BY SARIN.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 10)

Sites (8, 8)

SS Bonds (6, 6)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (32, 32)

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