5VDH - JenaLib

Title :   CRYSTAL STRUCTURE OF HUMAN GLYCINE RECEPTOR ALPHA-3 BOUND TO AM-3607, GLYCINE, AND IVERMECTIN

Authors :   P. L. Shaffer, X. Huang, H. Chen

Date :   03 Apr 17 (Deposition) - 24 May 17 (Release) - 21 Jun 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.85

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

Keywords :   Ligand-Gated Ion Channel, Neurotransmitter Receptor, Membrane Protein, Cys-Loop Receptor, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Huang, H. Chen, P. L. Shaffer
Crystal Structures Of Human Glyr Alpha 3 Bound To Ivermectin.
Structure V. 25 945 2017
PubMed-ID: 28479061 | Reference-DOI: 10.1016/J.STR.2017.04.007

Compounds

Molecule 1 - GLYCINE RECEPTOR SUBUNIT ALPHA-3
	Chains	:	A, B, C, D, E
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Common	:	FALL ARMYWORM
	Expression System Taxid	:	7108
	Fragment	:	UNP RESIDUES 34-342, ATG LINKER, UNP RESIDUES 419-460
	Gene	:	GLRA3
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Structural Features

Chains, Units

		1	2	3	4	5
Asymmetric/Biological Unit	:	A	B	C	D	E

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (6, 22)

Asymmetric/Biological Unit (6, 22)

No.	Name	Count	Type	Full Name
1	7C6	5	Ligand/Ion	(3S,3AS,9BS)-2-[(2H-1,3-BENZODIOXOL-5-YL)SULFONYL]-3,5-DIMETHYL-1,2,3,3A,5,9B-HEXAHYDRO-4H-PYRROLO[3,4-C][1,6]NAPHTHYRIDIN-4-ONE
2	CL	1	Ligand/Ion	CHLORIDE ION
3	GLY	5	Mod. Amino Acid	GLYCINE
4	IVM	5	Ligand/Ion	(2AE,4E,5'S,6S,6'R,7S,8E,11R,13R,15S,17AR,20R,20AR,20BS)-6'-[(2S)-BUTAN-2-YL]-20,20B-DIHYDROXY-5',6,8,19-TETRAMETHYL-17-OXO-3',4',5',6,6',10,11,14,15,17,17A,20,20A,20B-TETRADECAHYDRO-2H,7H-SPIRO[11,15-METHANOFURO[4,3,2-PQ][2,6]BENZODIOXACYCLOOCTADECINE-13,2'-PYRAN]-7-YL 2,6-DIDEOXY-4-O-(2,6-DIDEOXY-3-O-METHYL-ALPHA-L-ARABINO-HEXOPYRANOSYL)-3-O-METHYL-ALPHA-L-ARABINO-HEXOPYRANOSIDE
5	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
6	ZN	5	Ligand/Ion	ZINC ION

Sites (21, 21)

Asymmetric Unit (21, 21)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:27 , ARG A:29 , PHE A:32 , GLY A:160 , TYR A:161 , HOH A:512 , PHE B:13 , LEU B:83 , ASP B:84 , LEU B:85	binding site for residue 7C6 A 401
02	AC2	SOFTWARE	PHE A:159 , TYR A:202 , THR A:204 , PHE B:63 , ARG B:65 , SER B:129	binding site for residue GLY A 402
03	AC3	SOFTWARE	THR A:264 , SER A:267 , SER A:268 , ALA A:288 , LEU A:291 , ILE B:225 , GLN B:226 , ILE B:229 , PRO B:230 , LEU B:233	binding site for residue IVM A 403
04	AC4	SOFTWARE	GLU A:192 , ASP A:194 , HIS A:215	binding site for residue ZN A 404
05	AC5	SOFTWARE	ARG B:27 , ILE B:28 , ARG B:29 , GLY B:160 , TYR B:161 , HOH B:509 , PHE C:13 , LEU C:83 , ASP C:84 , LEU C:85	binding site for residue 7C6 B 401
06	AC6	SOFTWARE	PHE B:159 , THR B:204 , PHE C:63 , ARG C:65 , SER C:129 , HOH C:501	binding site for residue GLY B 402
07	AC7	SOFTWARE	THR B:264 , SER B:267 , SER B:268 , SER B:278 , ALA B:288 , LEU B:291 , ILE C:225 , GLN C:226 , ILE C:229 , PRO C:230 , LEU C:233	binding site for residue IVM B 403
08	AC8	SOFTWARE	GLU B:192 , ASP B:194 , HIS B:215	binding site for residue ZN B 404
09	AC9	SOFTWARE	ARG C:27 , ILE C:28 , ARG C:29 , PHE C:32 , GLY C:160 , TYR C:161 , HOH C:509 , PHE D:13 , ASP D:84 , LEU D:85 , ASP D:86	binding site for residue 7C6 C 401
10	AD1	SOFTWARE	PHE C:159 , TYR C:202 , THR C:204 , PHE D:63 , ARG D:65 , SER D:129	binding site for residue GLY C 402
11	AD2	SOFTWARE	THR C:264 , SER C:267 , SER C:268 , ALA C:288 , LEU C:291 , ILE D:225 , GLN D:226 , ILE D:229 , PRO D:230 , LEU D:233	binding site for residue IVM C 403
12	AD3	SOFTWARE	GLU C:192 , ASP C:194 , HIS C:215	binding site for residue ZN C 404
13	AD4	SOFTWARE	ARG D:27 , ILE D:28 , ARG D:29 , PHE D:32 , GLY D:160 , TYR D:161 , HOH D:506 , PRO E:10 , PHE E:13 , LEU E:14 , LEU E:83 , ASP E:84 , LEU E:85 , ASP E:86	binding site for residue 7C6 D 401
14	AD5	SOFTWARE	PHE D:159 , TYR D:202 , THR D:204 , HOH D:501 , PHE E:63 , ARG E:65 , SER E:129	binding site for residue GLY D 402
15	AD6	SOFTWARE	SER D:267 , SER D:268 , LEU D:291 , ILE E:225 , GLN E:226 , ILE E:229 , PRO E:230 , LEU E:233	binding site for residue IVM D 403
16	AD7	SOFTWARE	GLU D:192 , ASP D:194 , HIS D:215	binding site for residue ZN D 404
17	AD8	SOFTWARE	PRO A:10 , PHE A:13 , LEU A:14 , TYR A:78 , ASP A:84 , LEU A:85 , ASP A:86 , ARG E:27 , ILE E:28 , ARG E:29 , PHE E:32 , GLY E:160 , TYR E:161 , HOH E:507	binding site for residue 7C6 E 401
18	AD9	SOFTWARE	PHE A:63 , ARG A:65 , SER A:129 , PHE E:159 , THR E:204	binding site for residue GLY E 402
19	AE1	SOFTWARE	ILE A:225 , GLN A:226 , ILE A:229 , PRO A:230 , LEU A:233 , THR E:264 , SER E:267 , SER E:268 , SER E:278 , ALA E:288 , LEU E:291	binding site for residue IVM E 403
20	AE2	SOFTWARE	GLU E:192 , ASP E:194 , HIS E:215	binding site for residue ZN E 404
21	AE3	SOFTWARE	ASN C:38 , GLU C:169	binding site for Mono-Saccharide NAG C 405 bound to ASN C 38

SS Bonds (10, 10)

Asymmetric/Biological Unit

No.	Residues
1	A:138	-	A:152
2	A:198	-	A:209
3	B:138	-	B:152
4	B:198	-	B:209
5	C:138	-	C:152
6	C:198	-	C:209
7	D:138	-	D:152
8	D:198	-	D:209
9	E:138	-	E:152
10	E:198	-	E:209

Cis Peptide Bonds (10, 10)

Asymmetric/Biological Unit

No.	Residues
1	Val A:111	-	Thr A:112
2	Phe A:145	-	Pro A:146
3	Val B:111	-	Thr B:112
4	Phe B:145	-	Pro B:146
5	Val C:111	-	Thr C:112
6	Phe C:145	-	Pro C:146
7	Val D:111	-	Thr D:112
8	Phe D:145	-	Pro D:146
9	Val E:111	-	Thr E:112
10	Phe E:145	-	Pro E:146

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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:338
                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.............eeeeeeeeeeeeeeee....eeeeeeeeeeeee.hhhh.......eeeehhhhhhhh....eee..eeeee........eeeeee...eeeeeeeeeeeee...........eeeeeeeeee.......eeeee.....eee........eee....eeee..eee..eee.eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vdh A   8 MSPSDFLDKLMGRTSGYDARIRPNFKGPPVNVTCNIFINSFGSIAETTMDYRVNIFLRQKWNDPRLAYSEYPDDSLDLDPSMLDSIWKPDLFFANEKGANFHEVTTDNKLLRIFKNGNVLYSIRLTLTLSCPMDLKNFPMDVQTCIMQLESFGYTMNDLIFEWQDEAPVQVAEGLTLPQFLLKEEKDLRYCTKHYNTGKFTCIEVRFHLERQMGYYLIQMYIPSLLIVILSWVSFWINMDAAPARVALGITTVLTMTTQSSGSRASLPKVSYVKAIDIWMAVCLLFVFSALLEYAAVNFVSRAGTKVFIDRAKKIDTISRACFPLAFLIFNIFYWVIY 345
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337

Chain B from PDB  Type:PROTEIN  Length:343
                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh.............eeeeeeeeeeeeeeee....eeeeeeeeeeeee.hhhh.......eeeehhhhhhhh....eee..eeeee........eeeeee...eeeeeeeeeeeee...........eeeeeeeeee.......eeeee.....eee........eee....eeee..eee..eee.eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vdh B   6 APMSPSDFLDKLMGRTSGYDARIRPNFKGPPVNVTCNIFINSFGSIAETTMDYRVNIFLRQKWNDPRLAYSEYPDDSLDLDPSMLDSIWKPDLFFANEKGANFHEVTTDNKLLRIFKNGNVLYSIRLTLTLSCPMDLKNFPMDVQTCIMQLESFGYTMNDLIFEWQDEAPVQVAEGLTLPQFLLKEEKDLRYCTKHYNTGKFTCIEVRFHLERQMGYYLIQMYIPSLLIVILSWVSFWINMDAAPARVALGITTVLTMTTQSSGSRASLPKVSYVKAIDIWMAVCLLFVFSALLEYAAVNFVSRAGTKVFIDRAKKIDTISRACFPLAFLIFNIFYWVIYKIL 348
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345

Chain C from PDB  Type:PROTEIN  Length:338
                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.............eeeeeeeeeeeeeeee....eeeeeeeeeeeee.hhhh.......eeeehhhhhhhh....eee..eeeee........eeeeee...eeeeeeeeeeeee...........eeeeeeeeee.......eeeee.....eee........eee....eeee..eee..eee.eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vdh C   8 MSPSDFLDKLMGRTSGYDARIRPNFKGPPVNVTCNIFINSFGSIAETTMDYRVNIFLRQKWNDPRLAYSEYPDDSLDLDPSMLDSIWKPDLFFANEKGANFHEVTTDNKLLRIFKNGNVLYSIRLTLTLSCPMDLKNFPMDVQTCIMQLESFGYTMNDLIFEWQDEAPVQVAEGLTLPQFLLKEEKDLRYCTKHYNTGKFTCIEVRFHLERQMGYYLIQMYIPSLLIVILSWVSFWINMDAAPARVALGITTVLTMTTQSSGSRASLPKVSYVKAIDIWMAVCLLFVFSALLEYAAVNFVSRAGTKVFIDRAKKIDTISRACFPLAFLIFNIFYWVIY 345
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337

Chain D from PDB  Type:PROTEIN  Length:343
                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhh.............eeeeeeeeeeeeeeee....eeeeeeeeeeeee.hhhh.......eeeehhhhhhhh....eee..eeeee........eeeeee...eeeeeeeeeeeee...........eeeeeeeeee.......eeeee.....eee........eee....eeee..eee..eee.eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vdh D   3 SRSAPMSPSDFLDKLMGRTSGYDARIRPNFKGPPVNVTCNIFINSFGSIAETTMDYRVNIFLRQKWNDPRLAYSEYPDDSLDLDPSMLDSIWKPDLFFANEKGANFHEVTTDNKLLRIFKNGNVLYSIRLTLTLSCPMDLKNFPMDVQTCIMQLESFGYTMNDLIFEWQDEAPVQVAEGLTLPQFLLKEEKDLRYCTKHYNTGKFTCIEVRFHLERQMGYYLIQMYIPSLLIVILSWVSFWINMDAAPARVALGITTVLTMTTQSSGSRASLPKVSYVKAIDIWMAVCLLFVFSALLEYAAVNFVSRAGTKVFIDRAKKIDTISRACFPLAFLIFNIFYWVIY 345
                                    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

Chain E from PDB  Type:PROTEIN  Length:338
                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.............eeeeeeeeeeeeeeee....eeeeeeeeeeeee.hhhh.......eeeehhhhhhhh....eee..eeeee........eeeeee...eeeeeeeeeeeee...........eeeeeeeeee.......eeeee.....eee........eee....eeee..eee..eee.eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vdh E   8 MSPSDFLDKLMGRTSGYDARIRPNFKGPPVNVTCNIFINSFGSIAETTMDYRVNIFLRQKWNDPRLAYSEYPDDSLDLDPSMLDSIWKPDLFFANEKGANFHEVTTDNKLLRIFKNGNVLYSIRLTLTLSCPMDLKNFPMDVQTCIMQLESFGYTMNDLIFEWQDEAPVQVAEGLTLPQFLLKEEKDLRYCTKHYNTGKFTCIEVRFHLERQMGYYLIQMYIPSLLIVILSWVSFWINMDAAPARVALGITTVLTMTTQSSGSRASLPKVSYVKAIDIWMAVCLLFVFSALLEYAAVNFVSRAGTKVFIDRAKKIDTISRACFPLAFLIFNIFYWVIY 345
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337

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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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (29, 29)

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	Cis Peptide Bonds
		Phe A:145 - Pro A:146	[ RasMol ]
		Phe B:145 - Pro B:146	[ RasMol ]
		Phe C:145 - Pro C:146	[ RasMol ]
		Phe D:145 - Pro D:146	[ RasMol ]
		Phe E:145 - Pro E:146	[ RasMol ]
		Val A:111 - Thr A:112	[ RasMol ]
		Val B:111 - Thr B:112	[ RasMol ]
		Val C:111 - Thr C:112	[ RasMol ]
		Val D:111 - Thr D:112	[ RasMol ]
		Val E:111 - Thr E:112	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 22)

Sites (21, 21)

SS Bonds (10, 10)

Cis Peptide Bonds (10, 10)

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