5U6E - JenaLib

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Title :   CRYSTAL STRUCTURE OF CLADE A/E HIV-1 GP120 CORE IN COMPLEX WITH NBD-14010

Authors :   Y. D. Kwon, A. K. Debnath, P. D. Kwong

Date :   07 Dec 16 (Deposition) - 22 Mar 17 (Release) - 26 Apr 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Hiv-1, Nbd-14010, Virus Entry Antagonist, Small Molecule, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Curreli, Y. D. Kwon, D. S. Belov, R. R. Ramesh, A. V. Kurkin, A. Altieri, P. D. Kwong, A. K. Debnath
Synthesis, Antiviral Potency, In Vitro Admet, And X-Ray Structure Of Potent Cd4 Mimics As Entry Inhibitors That Target The Phe43 Cavity Of Hiv-1 Gp120.
J. Med. Chem. V. 60 3124 2017
PubMed-ID: 28266845 | Reference-DOI: 10.1021/ACS.JMEDCHEM.7B00179

Molecule 1 - CLADE A/E 93TH057 HIV-1 GP120 CORE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Atcc Number	:	CRL-3022
	Expression System Cell Line	:	HEK 293 GNTI-
	Expression System Common	:	HUMAN
	Expression System Plasmid	:	PVRC8400
	Expression System Taxid	:	9606
	Expression System Vector Type	:	PLASMID
	Gene	:	HIV-1 ENV
	Organism Scientific	:	HUMAN IMMUNODEFICIENCY VIRUS 1
	Organism Taxid	:	11676
	Other Details	:	CLADE A/E 93TH057 HIV-1 GP120 CORE, V1/V2 AND V3 REGION DELETION, H375S

		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 (3, 22)

No.	Name	Count	Type	Full Name
1	82M	2	Ligand/Ion	N-{(1S)-2-AMINO-1-[5-(HYDROXYMETHYL)-4-METHYL-1,3-THIAZOL-2-YL]ETHYL}-5-(4-CHLORO-3-FLUOROPHENYL)-1H-PYRROLE-2-CARBOXAMIDE
2	EPE	2	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3	NAG	18	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (3, 13)

No.	Name	Count	Type	Full Name
1	82M	1	Ligand/Ion	N-{(1S)-2-AMINO-1-[5-(HYDROXYMETHYL)-4-METHYL-1,3-THIAZOL-2-YL]ETHYL}-5-(4-CHLORO-3-FLUOROPHENYL)-1H-PYRROLE-2-CARBOXAMIDE
2	EPE	1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3	NAG	11	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 2 (3, 9)

No.	Name	Count	Type	Full Name
1	82M	1	Ligand/Ion	N-{(1S)-2-AMINO-1-[5-(HYDROXYMETHYL)-4-METHYL-1,3-THIAZOL-2-YL]ETHYL}-5-(4-CHLORO-3-FLUOROPHENYL)-1H-PYRROLE-2-CARBOXAMIDE
2	EPE	1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3	NAG	7	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (22, 22)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	VAL A:255 , SER A:256 , THR A:257 , ASP A:368 , GLU A:370 , SER A:375 , PHE A:376 , PHE A:382 , ASN A:425 , MET A:426 , TRP A:427 , GLY A:429 , GLY A:473 , HOH A:683 , HOH A:684	binding site for residue 82M A 512
02	AC2	SOFTWARE	LEU A:52 , CYS A:54 , HIS A:72 , ALA A:73 , GLN A:103 , ASP A:107 , HOH A:611	binding site for residue EPE A 513
03	AC3	SOFTWARE	VAL B:255 , SER B:256 , ASP B:368 , GLU B:370 , SER B:375 , PHE B:376 , PHE B:382 , ASN B:425 , MET B:426 , TRP B:427	binding site for residue 82M B 508
04	AC4	SOFTWARE	LEU B:52 , CYS B:54 , ALA B:73 , GLN B:103 , ASP B:107 , TYR B:217	binding site for residue EPE B 509
05	AC5	SOFTWARE	ASN A:234 , SER A:274 , HIS A:352 , HOH A:663	binding site for Mono-Saccharide NAG A 501 bound to ASN A 234
06	AC6	SOFTWARE	ASP A:230 , LYS A:231 , ASN A:241	binding site for Mono-Saccharide NAG A 502 bound to ASN A 241
07	AC7	SOFTWARE	LEU A:261 , ASN A:262 , ARG A:379 , CYS A:445 , VAL A:446 , SER A:447 , HOH A:616 , HOH A:635 , HOH A:681	binding site for Mono-Saccharide NAG A 503 bound to ASN A 262
08	AC8	SOFTWARE	ASN A:276 , ASN A:279 , HIS B:61 , HOH B:620	binding site for Mono-Saccharide NAG A 504 bound to ASN A 276
09	AC9	SOFTWARE	GLU A:268 , GLU A:269 , ILE A:270 , ASN A:289 , LYS A:348 , HOH A:631	binding site for Mono-Saccharide NAG A 505 bound to ASN A 289
10	AD1	SOFTWARE	ASN A:295 , TYR A:330 , GLU A:332 , HOH A:658	binding site for Mono-Saccharide NAG A 506 bound to ASN A 295
11	AD2	SOFTWARE	ASN A:334 , LYS A:337 , HOH A:633	binding site for Mono-Saccharide NAG A 507 bound to ASN A 334
12	AD3	SOFTWARE	GLU A:351 , ASN A:354 , ASN A:355 , PRO B:214 , LYS B:252	binding site for Mono-Saccharide NAG A 508 bound to ASN A 355
13	AD4	SOFTWARE	ASN A:386 , THR A:388 , HOH A:692	binding site for Mono-Saccharide NAG A 509 bound to ASN A 386
14	AD5	SOFTWARE	SER A:291 , ASN A:448 , HOH A:685	binding site for Mono-Saccharide NAG A 510 bound to ASN A 448
15	AD6	SOFTWARE	THR A:278 , ASN A:461 , GLU B:62 , HOH B:620	binding site for Mono-Saccharide NAG A 511 bound to ASN A 461
16	AD7	SOFTWARE	ASN B:234 , THR B:236	binding site for Mono-Saccharide NAG B 501 bound to ASN B 234
17	AD8	SOFTWARE	ASN B:229 , ASN B:241	binding site for Mono-Saccharide NAG B 502 bound to ASN B 241
18	AD9	SOFTWARE	ASN A:354 , ASN A:355 , SER A:464 , LYS B:252 , ASN B:262 , ARG B:379 , CYS B:445 , VAL B:446 , SER B:447 , HOH B:611 , HOH B:628 , HOH B:630 , HOH B:634	binding site for Mono-Saccharide NAG B 503 bound to ASN B 262
19	AE1	SOFTWARE	GLU B:269 , ILE B:270 , ASN B:289 , GLN B:344 , LYS B:348	binding site for Mono-Saccharide NAG B 504 bound to ASN B 289
20	AE2	SOFTWARE	ASN B:295 , TYR B:330 , GLU B:332 , HOH B:646	binding site for Mono-Saccharide NAG B 505 bound to ASN B 295
21	AE3	SOFTWARE	ASN B:334 , LYS B:337 , THR B:413	binding site for Mono-Saccharide NAG B 506 bound to ASN B 334
22	AE4	SOFTWARE	ASN B:386 , THR B:388 , HOH B:603	binding site for Mono-Saccharide NAG B 507 bound to ASN B 386

Asymmetric Unit

No.	Residues
1	A:54	-	A:74
2	A:119	-	A:205
3	A:218	-	A:247
4	A:228	-	A:239
5	A:296	-	A:331
6	A:378	-	A:445
7	A:385	-	A:418
8	A:395	-	A:410
9	B:54	-	B:74
10	B:119	-	B:205
11	B:218	-	B:247
12	B:228	-	B:239
13	B:296	-	B:331
14	B:378	-	B:445
15	B:385	-	B:418
16	B:395	-	B:410

(no "Cis Peptide Bond" information available for 5U6E)

(no "SAP(SNP)/Variant" information available for 5U6E)

(no "PROSITE Motif" information available for 5U6E)

(no "Exon" information available for 5U6E)

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

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	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:340
                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eeee.......hhhhhhhhhhhee......eeee....eeee...hhhhhhhhhhhhhhhhhhh...eeee..eeee.............eee....eeeeee.......eeee..eeee.............eee.........eee..........eeeeeeeeeeeeeee.......eeeeeeehhhhhhhhhhhhhhhhhhh...eeee......hhhhhheeeee..eeeee..............eeeeeeeee.eee......eee........eeeeeeeeeeeeee........eeeeee...hhhhhhhhhhh.eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u6e A  44 VWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVISLWDQSLQPCVKLTGGSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINCTRPSNGDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITMHSFNCRGEFFYCNTTQLFNNTCICNGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNITGILLTRDGGANNTSNETFRPGGGNIKDNWRSELYKYKVVQIE 492
                                    53        63        73        83        93       103       113       123||     206       216       226       236       246       256       266       276       286       296    || 328       338       348      |359       369       379       389      |412       422       432       442       452       462       472       482       492
                                                                                                          124|                                                                                                    301|                            355|                                    396|                                                                                  
                                                                                                           198                                                                                                     324                             357                                     410

Chain B from PDB  Type:PROTEIN  Length:340
                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eeee.......hhhhhhhhhhhee.......eee....eeee...hhhhhhhhhhhhhhhhhhh...eeee..eeee.............eee....eeeeee.......eeee..eeee.............eee.........eee..........eeeeeeeeeeeeeee.......eeeeeeehhhhhhhhhhhhhhhhhhh...eeee......hhhhhheeeee..eeeee.hhhhhhhhhh...eeeeeeee..eeee....eeee........eeeeeeeeeeeeee........eeeeee...hhhhhhhhhhh.eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u6e B  44 VWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVISLWDQSLQPCVKLTGGSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINCTRPSNGDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITMHSFNCRGEFFYCNTTQLFNNTCICNGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNITGILLTRDGGANNTSNETFRPGGGNIKDNWRSELYKYKVVQIE 492
                                    53        63        73        83        93       103       113       123||     206       216       226       236       246       256       266       276       286       296    || 328       338       348      |359       369       379       389      |412       422       432       442       452       462       472       482       492
                                                                                                          124|                                                                                                    301|                            355|                                    396|                                                                                  
                                                                                                           198                                                                                                     324                             357                                     410

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Description

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Chains, Units

Ligands, Modified Residues, Ions (3, 22)

Sites (22, 22)

SS Bonds (16, 16)

Cis Peptide Bonds (0, 0)

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