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Description

Title :   CRYSTAL STRUCTURE OF MULTIDRUG RESISTANT HIV-1 PROTEASE CLINICAL ISOLATE PR20 WITH THE POTENT ANTIVIRAL INHIBITOR GRL-0519A

Authors :   Y. -F. Wang, J. Agniswamy, I. T. Weber

Date :   07 Feb 13 (Deposition) - 15 May 13 (Release) - 05 Jun 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.55

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

Keywords :   Multidrug Resistant Hiv-1 Protease Clinical Isolate Pr20, Clinical Inhibitor Amprenavir, Potent Antiviral Inhibitor Grl-0519A, Potent Antiviral Inhibitor Grl-02031, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Agniswamy, C. H. Shen, Y. F. Wang, A. K. Ghosh, K. V. Rao, C. X. Xu, J. M. Sayer, J. M. Louis, I. T. Weber
Extreme Multidrug Resistant Hiv-1 Protease With 20 Mutation Is Resistant To Novel Protease Inhibitors With P1'-Pyrrolidinone Or P2-Tris-Tetrahydrofuran.
J. Med. Chem. V. 56 4017 2013
PubMed-ID: 23590295 | Reference-DOI: 10.1021/JM400231V

Compounds

Molecule 1 - PROTEASE
	Chains	:	A, B
	EC Number	:	3.4.23.16
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 501-599
	Gene	:	POL
	Mutation	:	YES
	Organism Common	:	HIV-1
	Organism Scientific	:	HUMAN IMMUNODEFICIENCY VIRUS 1
	Organism Taxid	:	11676

Structural Features

Chains, Units

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (3, 25)

Asymmetric/Biological Unit (3, 25)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	G52	2	Ligand/Ion	(3R,3AS,3BR,6AS,7AS)-OCTAHYDRODIFURO[2,3-B:3',2'-D]FURAN-3-YL [(1S,2R)-1-BENZYL-2-HYDROXY-3-{[(4-METHOXYPHENYL)SULFONYL](2-METHYLPROPYL)AMINO}PROPYL]CARBAMATE
3	IOD	22	Ligand/Ion	IODIDE ION

Sites (22, 22)

Asymmetric Unit (22, 22)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:25 , GLY A:27 , ALA A:28 , ASP A:29 , ASN A:30 , GLY A:48 , ILE A:50 , VAL A:82 , ASP B:25 , GLY B:27 , ALA B:28 , ASP B:29 , ASN B:30 , ILE B:32 , GLY B:48 , GLY B:49 , ILE B:50 , VAL B:82 , HOH B:1001	BINDING SITE FOR RESIDUE G52 A 201
02	AC2	SOFTWARE	ASP A:35 , ASN A:83	BINDING SITE FOR RESIDUE IOD A 202
03	AC3	SOFTWARE	G52 B:101	BINDING SITE FOR RESIDUE IOD A 203
04	AC4	SOFTWARE	ACT A:216	BINDING SITE FOR RESIDUE IOD A 204
05	AC5	SOFTWARE	THR A:12 , IOD A:206	BINDING SITE FOR RESIDUE IOD A 205
06	AC6	SOFTWARE	IOD A:205	BINDING SITE FOR RESIDUE IOD A 206
07	AC7	SOFTWARE	GLU A:21 , ASN A:83	BINDING SITE FOR RESIDUE IOD A 207
08	AC8	SOFTWARE	GLU A:21 , VAL A:82 , HOH A:340 , ARG B:8	BINDING SITE FOR RESIDUE IOD A 208
09	AC9	SOFTWARE	GLU A:65	BINDING SITE FOR RESIDUE IOD A 209
10	BC1	SOFTWARE	THR A:4	BINDING SITE FOR RESIDUE IOD A 210
11	BC2	SOFTWARE	ARG B:8	BINDING SITE FOR RESIDUE IOD A 211
12	BC3	SOFTWARE	LYS A:14 , GLY A:16 , GLY A:17 , PRO A:63 , HOH A:344	BINDING SITE FOR RESIDUE IOD A 212
13	BC4	SOFTWARE	PRO A:44 , HOH A:338	BINDING SITE FOR RESIDUE IOD A 214
14	BC5	SOFTWARE	GLN A:61 , HOH A:341	BINDING SITE FOR RESIDUE IOD A 215
15	BC6	SOFTWARE	PHE A:53 , ARG A:57 , IOD A:204	BINDING SITE FOR RESIDUE ACT A 216
16	BC7	SOFTWARE	IOD A:203 , VAL B:56 , THR B:91 , GLY B:94 , HOH B:1024	BINDING SITE FOR RESIDUE G52 B 101
17	BC8	SOFTWARE	ASP B:35 , GLY B:78	BINDING SITE FOR RESIDUE IOD B 102
18	BC9	SOFTWARE	GLU B:21	BINDING SITE FOR RESIDUE IOD B 103
19	CC1	SOFTWARE	ALA B:67	BINDING SITE FOR RESIDUE IOD B 106
20	CC2	SOFTWARE	THR B:12 , HOH B:1041 , HOH B:1042	BINDING SITE FOR RESIDUE IOD B 107
21	CC3	SOFTWARE	MET B:46	BINDING SITE FOR RESIDUE IOD B 108
22	CC4	SOFTWARE	PRO B:39 , GLY B:40	BINDING SITE FOR RESIDUE IOD B 109

SS Bonds (0, 0)

(no "SS Bond" information available for 4J54)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 4J54)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 4J54)

PROSITE Motifs (0, 0)

(no "PROSITE Motif" information available for 4J54)

Exons (0, 0)

(no "Exon" information available for 4J54)

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:99
                                                                                                                                  
               SCOP domains d4j54a_ A: Human immunodeficiency virus type 1 protease                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eeeeee..eeeeeee.......ee.........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeee......eehhhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  4j54 A  1 PQITLWKRPFVTVKVGGQLKEALLDTGADNTIFEDINLPGRWKPKMVGGIGGFLKVREYDQVPIEIAGHKVIGTVLVGPTPVNVIGRDTMTQIGATLNF 99
                                    10        20        30        40        50        60        70        80        90

Chain B from PDB  Type:PROTEIN  Length:99
                                                                                                                                  
               SCOP domains d4j54b_ B: Human immunodeficiency virus type 1 protease                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eeeeee..eeeeeee.......ee.........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeee......eehhhhhhh...eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  4j54 B  1 PQITLWKRPFVTVKVGGQLKEALLDTGADNTIFEDINLPGRWKPKMVGGIGGFLKVREYDQVPIEIAGHKVIGTVLVGPTPVNVIGRDTMTQIGATLNF 99
                                    10        20        30        40        50        60        70        80        90

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 '\|'

Classification and Annotation

SCOP Domains (1, 2)

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Acid proteases (1120)

Superfamily: Acid proteases (1120)

Family: Retroviral protease (retropepsin) (591)

Protein domain: Human immunodeficiency virus type 1 protease (514)

Human immunodeficiency virus type 1 [TaxId: 11676] (424)

1a	d4j54a_	A:
1b	d4j54b_	B:

CATH Domains (0, 0)

(no "CATH Domain" information available for 4J54)

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 4J54)

Gene Ontology (45, 45)

Asymmetric/Biological Unit(hide GO term definitions)

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	Cis Peptide Bonds
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	4j54
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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	POL_HV1BR \| P03367	:	1a8g 1a8k 1a94 1aaq 1d4s 1d4y 1daz 1dif 1fqx 1hhp 1hni 1hpo 1hpx 1hsg 1hvl 1iiq 1izi 1lzq 1m0b 1mrw 1mrx 1msm 1msn 1nh0 1rl8 1sdt 1sdu 1sdv 1sgu 1sh9 1sp5 1u8g 1upj 1xl2 1xl5 1z8c 1zbg 1zj7 1zlf 1zpk 1zsf 1zsr 1ztz 2a1e 2az8 2az9 2azb 2azc 2b7z 2bb9 2fde 2fnd 2hb2 2hb4 2hc0 2hnd 2hny 2ien 2o4k 2o4l 2o4n 2o4p 2o4s 2p3b 2pk5 2pk6 2pqz 2pwc 2pwr 2pym 2pyn 2q63 2q64 2qak 2qci 2qd6 2qd7 2qd8 2qhc 2qnn 2qnp 2qnq 2r43 2upj 2z4o 2zga 2zye 3a2o 3bc4 3bgb 3bgc 3bhe 3bva 3bvb 3ckt 3djk 3dk1 3fx5 3ggu 3h5b 3i6o 3i8w 3jvw 3jvy 3jw2 3kdb 3kdc 3kdd 3ndu 3ndw 3ndx 3nls 3psu 3pwm 3pwr 3qbf 3qih 3qn8 3qp0 3qpj 3qrm 3qro 3qrs 3st5 3t11 3t3c 3tkg 3tkw 3tl9 3tof 3tog 3toh 3ttp 3u7s 3ucb 3uf3 3ufn 3uhl 3vf5 3vf7 3vfb 4dfg 4faf 4fe6 4fl8 4flg 4fm6 4gb2 4hdb 4hdf 4hdp 4he9 4heg 4hla 4j55 4j5j 4jec 4ll3 5e5k 7upj

Related Entries Specified in the PDB File

3ok9	CRYSTAL STRUCTURE OF WILD-TYPE HIV-1 PROTEASE WITH THE POTENT ANTIVIRAL INHIBITOR GRL-0519A
3ucb	CRYSTAL STRUCTURE OF MULTIDRUG RESISTANT HIV-1 PROTEASE CLINICAL ISOLATE PR20 WITH DARUNAVIR
3uf3	CRYSTAL STRUCTURE OF MULTIDRUG RESISTANT HIV-1 PROTEASE CLINICAL ISOLATE PR20 WITH YTTRIUM(III) CHLORIDE
3ufn	CRYSTAL STRUCTURE OF MULTIDRUG RESISTANT HIV-1 PROTEASE CLINICAL ISOLATE PR20 WITH SAQUINAVIR
3uhl	CRYSTAL STRUCTURE OF MULTIDRUG RESISTANT HIV-1 PROTEASE CLINICAL ISOLATE PR20 WITH THE P2-NC SUBSTRATE ANALOG
4j55
4j5j