4I53 - JenaLib

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Title :   CRYSTAL STRUCTURE OF CLADE C1086 HIV-1 GP120 CORE IN COMPLEX WITH DMJ-II-121

Authors :   M. Le-Khac, W. A. Hendrickson

Date :   28 Nov 12 (Deposition) - 29 May 13 (Release) - 29 May 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Hiv, Gp120, Entry Inhibitor, Dmj-Ii-121, Cd4-Mimetic, Viral Protein- Inhibitor Complex, C1086, Extracellular (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. M. Lalonde, M. Le-Khac, D. M. Jones, J. R. Courter, J. Park, A. Schon, A. M. Princiotto, X. Wu, J. R. Mascola, E. Freire, J. Sodroski, N. Madani, W. A. Hendrickson, A. B. Smith
Structure-Based Design And Synthesis Of An Hiv-1 Entry Inhibitor Exploiting X-Ray And Thermodynamic Characterization.
Acs Med Chem Lett V. 4 338 2013
PubMed-ID: 23667716 | Reference-DOI: 10.1021/ML300407Y

Molecule 1 - HIV-1 GLYCOPROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Plasmid	:	PVRC8400
	Expression System Strain	:	293F
	Expression System Taxid	:	9606
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	HUMAN IMMUNODEFICIENCY VIRUS TYPE 1
	Organism Taxid	:	11676
	Strain	:	C1086

		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, 16)

No.	Name	Count	Type	Full Name
1	1C1	2	Ligand/Ion	AMINO({[(1R,2R)-1-({[(4-CHLORO-3-FLUOROPHENYL)AMINO](OXO)ACETYL}AMINO)-2,3-DIHYDRO-1H-INDEN-2-YL]METHYL}AMINO)METHANIMINIUM
2	FMT	1	Ligand/Ion	FORMIC ACID
3	NAG	13	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	1C1	1	Ligand/Ion	AMINO({[(1R,2R)-1-({[(4-CHLORO-3-FLUOROPHENYL)AMINO](OXO)ACETYL}AMINO)-2,3-DIHYDRO-1H-INDEN-2-YL]METHYL}AMINO)METHANIMINIUM
2	FMT	-1	Ligand/Ion	FORMIC ACID
3	NAG	7	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 2 (3, 8)

No.	Name	Count	Type	Full Name
1	1C1	1	Ligand/Ion	AMINO({[(1R,2R)-1-({[(4-CHLORO-3-FLUOROPHENYL)AMINO](OXO)ACETYL}AMINO)-2,3-DIHYDRO-1H-INDEN-2-YL]METHYL}AMINO)METHANIMINIUM
2	FMT	1	Ligand/Ion	FORMIC ACID
3	NAG	6	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	SER A:256 , THR A:257 , GLU A:370 , SER A:375 , PHE A:376 , ASN A:425 , MET A:426 , TRP A:427 , GLU A:429 , VAL A:430 , GLY A:431 , GLY A:472 , GLY A:473 , MET A:475 , HOH A:620 , HOH A:678 , HOH A:760	BINDING SITE FOR RESIDUE 1C1 A 501
02	AC2	SOFTWARE	ASN A:234 , THR A:236 , PRO A:238 , LEU A:277 , HIS A:352 , HOH A:696	BINDING SITE FOR RESIDUE NAG A 502
03	AC3	SOFTWARE	LYS A:252 , ASN A:262 , CYS A:445 , ASN A:446 , SER A:447 , HOH A:601 , HOH A:608 , HOH A:614 , HOH A:690 , HOH A:750	BINDING SITE FOR RESIDUE NAG A 503
04	AC4	SOFTWARE	ASN A:276 , THR A:278 , ASN A:279 , THR B:278 , NAG B:505	BINDING SITE FOR RESIDUE NAG A 504
05	AC5	SOFTWARE	GLU A:269 , ILE A:270 , ASN A:289 , LYS A:344 , GLU A:348	BINDING SITE FOR RESIDUE NAG A 505
06	AC6	SOFTWARE	GLU A:335 , SER A:336 , ASN A:339 , SER A:409 , GLY A:412 , HOH A:688	BINDING SITE FOR RESIDUE NAG A 506
07	AC7	SOFTWARE	THR A:372 , THR A:373 , ASN A:386 , SER A:388 , HOH A:602	BINDING SITE FOR RESIDUE NAG A 507
08	AC8	SOFTWARE	PRO A:363 , ASP A:389 , ASN A:392 , ARG A:396 , ASN A:404 , THR A:406 , GLY A:407	BINDING SITE FOR RESIDUE NAG A 508
09	AC9	SOFTWARE	VAL B:255 , SER B:256 , GLU B:370 , SER B:375 , PHE B:376 , ILE B:424 , ASN B:425 , MET B:426 , TRP B:427 , GLU B:429 , VAL B:430 , GLY B:431 , GLY B:473 , MET B:475 , FMT B:502 , HOH B:696	BINDING SITE FOR RESIDUE 1C1 B 501
10	BC1	SOFTWARE	ASN B:425 , GLY B:431 , ARG B:432 , 1C1 B:501	BINDING SITE FOR RESIDUE FMT B 502
11	BC2	SOFTWARE	ASN B:234 , THR B:236 , LEU B:277 , HIS B:352	BINDING SITE FOR RESIDUE NAG B 503
12	BC3	SOFTWARE	LYS A:59 , LYS B:252 , ASN B:262 , CYS B:445 , SER B:447 , HOH B:619 , HOH B:627 , HOH B:670 , HOH B:673	BINDING SITE FOR RESIDUE NAG B 504
13	BC4	SOFTWARE	GLU A:275 , LYS A:282 , NAG A:504 , ASN B:276 , THR B:278	BINDING SITE FOR RESIDUE NAG B 505
14	BC5	SOFTWARE	GLU B:268 , GLU B:269 , ILE B:270 , ASN B:289 , GLU B:290 , LYS B:344 , GLU B:348 , HOH B:680	BINDING SITE FOR RESIDUE NAG B 506
15	BC6	SOFTWARE	THR B:372 , ASN B:386 , SER B:388 , HOH B:608 , HOH B:681	BINDING SITE FOR RESIDUE NAG B 507
16	BC7	SOFTWARE	ASP B:389 , ASN B:392 , THR B:406 , GLY B:407 , ARG B:408	BINDING SITE FOR RESIDUE NAG B 508

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	B:54	-	B:74
9	B:119	-	B:205
10	B:218	-	B:247
11	B:228	-	B:239
12	B:296	-	B:331
13	B:378	-	B:445
14	B:385	-	B:418

(no "Cis Peptide Bond" information available for 4I53)

(no "SAP(SNP)/Variant" information available for 4I53)

(no "PROSITE Motif" information available for 4I53)

(no "Exon" information available for 4I53)

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
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Chain A from PDB  Type:PROTEIN  Length:336
                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee.......hhhhhhhhhhhee.......eee....eeee...hhhhhhhhhhhhhhhhhhh...eeee..eeee.............eee....eeeeee.......eeee..eeee.............eee.........eeee.........eeeeeeeeeeeeeee.....eeeeeeehhhhhhhhhhhhhhhhhhh...eeee......hhhhhheeeee..eeeee.......eeee..eeee.......eeeeeee...eee......eee........eeeeeeeeeeeeee..eeeeee....hhhhhhhhhh.eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4i53 A  49 KTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEMVLANVTENFNMWKNDMVEQMHEDIISLWDESLKPCVKLTGGSAITQACPKVSFDPIPLHYCAPAGFAILKCNNKTFNGTGPCRNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNESVNIVCTRPNNIRQAHCNINESKWNNTLQKVGEELAKHFPSKTIKFEPSSGGDLEITTHSFNCRGEFFYCNTSDLFNGTYRNGTYNHTGRSSNGTITLQCKIKQIINMWQEVGRAIYAPPIEGEITCNSNITGLLLLRDDTETFRPGGGDMRDNWRSELYKYKVVEI 491
                                    58        68        78        88        98       108       118     ||201       211       221       231       241       251       261       271       281       291       325       335       345       356       366       376       386       396  ||   409       419       429       439       449       465       475       485      
                                                                                                     124|                                                                                                   300|                          354|                                        399|                                                   457|                           
                                                                                                      198                                                                                                    325                           356                                         403                                                    464

Chain B from PDB  Type:PROTEIN  Length:335
                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee.......hhhhhhhhhhhee..............eeee...hhhhhhhhhhhhhhhhhhh...eeee..eeee.............eee.....eeeee.......eeee..eeee.............eee.........eeee.........eeeeeeeeeeeeeee.....eeeeeeehhhhhhhhhhhhhhhhhhh...eeee......hhhhhheeeee..eeeee.......eeee..eeee.......eeeeeeee..eee......eee........eeeeeeeeeeeeee..eeeeee....hhhhhhhhhh.eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i53 B  49 KTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEMVLANVTENFNMWKNDMVEQMHEDIISLWDESLKPCVKLTGGSAITQACPKVSFDPIPLHYCAPAGFAILKCNNKTFNGTGPCRNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNESVNIVCTRPNNIRQAHCNINESKWNNTLQKVGEELAKHFPSKTIKFEPSSGGDLEITTHSFNCRGEFFYCNTSDLFNGTYRNGTYNHTGRSSNGTITLQCKIKQIINMWQEVGRAIYAPPIEGEITCNSNITGLLLLRDDTETFRPGGGDMRDNWRSELYKYKVVE 490
                                    58        68        78        88        98       108       118     ||201       211       221       231       241       251       261       271       281       291       325       335       345       356       366       376       386       396  ||   409       419       429       439       449       465       475       485     
                                                                                                     124|                                                                                                   300|                          354|                                        399|                                                   457|                          
                                                                                                      198                                                                                                    325                           356                                         403                                                    464

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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 4I53)

(no "CATH Domain" information available for 4I53)

(no "Pfam Domain" information available for 4I53)

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 16)

Sites (16, 16)

SS Bonds (14, 14)

Cis Peptide Bonds (0, 0)

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