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Title :   CRYSTAL STRUCTURE OF THE ADCC-POTENT ANTIBODY N60-I3 FAB IN COMPLEX WITH HIV-1 CLADE A/E GP120 W69A/S115W MUTANT AND M48U1.

Authors :   W. D. Tolbert, M. Pazgier

Date :   20 Jun 16 (Deposition) - 20 Jul 16 (Release) - 26 Oct 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.98

Chains :   Asym./Biol. Unit : G,H,L,N

Keywords :   Hiv-1 Gp120, Clade A/E 93Th057, Viral Protein, Viral Protein-Immune System-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Ding, W. D. Tolbert, J. Prevost, B. Pacheco, M. Coutu, O. Debbeche, S. H. Xiang, M. Pazgier, A. Finzi
A Highly Conserved Gp120 Inner Domain Residue Modulates Env Conformation And Trimer Stability.
J. Virol. V. 90 8395 2016
PubMed-ID: 27384653 | Reference-DOI: 10.1128/JVI.01068-16

Molecule 1 - CLADE A/E 93TH057 HIV-1 GP120 CORE
	Chains	:	G
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK 293 GNT1- CELLS
	Expression System Taxid	:	9606
	Expression System Vector Type	:	PLASMID
	Gene	:	HIV-1 ENV
	Mutation	:	YES
	Organism Scientific	:	HUMAN IMMUNODEFICIENCY VIRUS 1
	Organism Taxid	:	11676

Molecule 2 - M48U1 CD4 MIMETIC PEPTIDE
	Chains	:	N
	Engineered	:	YES
	Organism Scientific	:	SYNTHETIC CONSTRUCT
	Organism Taxid	:	32630
	Synthetic	:	YES

Molecule 3 - N60-I3 FAB HEAVY CHAIN
	Chains	:	H
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK 293 CELLS
	Expression System Taxid	:	9606
	Expression System Vector Type	:	PLASMID
	Gene	:	FAB HEAVY CHAIN OF ADCC-POTENT ANTI-HIV-1 ANTIBODY N60-I3
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 4 - N60-I3 FAB LIGHT CHAIN
	Chains	:	L
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK 293 CELLS
	Expression System Taxid	:	9606
	Expression System Vector Type	:	PLASMID
	Gene	:	FAB LIGHT CHAIN OF ADCC-POTENT ANTI-HIV-1 ANTIBODY N60-I3
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2	3	4
Asymmetric/Biological Unit	:	G	H	L	N

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (6, 15)

No.	Name	Count	Type	Full Name
1	DPR	1	Mod. Amino Acid	D-PROLINE
2	MPD	1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	MPT	1	Mod. Amino Acid	BETA-MERCAPTOPROPIONIC ACID
4	NAG	10	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	NH2	1	Mod. Amino Acid	AMINO GROUP
6	U2X	1	Mod. Amino Acid	O-(CYCLOHEXYLMETHYL)-L-TYROSINE

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLY H:42 , ASP L:85 , TYR L:87 , GLY L:100 , LYS L:103	binding site for residue MPD L 301
02	AC2	SOFTWARE	ASN G:234 , SER G:274 , LEU G:277	binding site for Mono-Saccharide NAG G 501 bound to ASN G 234
03	AC3	SOFTWARE	LYS G:231 , ASN G:241 , NAG G:506	binding site for Mono-Saccharide NAG G 502 bound to ASN G 241
04	AC4	SOFTWARE	ASP G:211 , LYS G:252 , ASN G:262 , ASN G:377 , VAL G:446 , SER G:447	binding site for Mono-Saccharide NAG G 503 bound to ASN G 262
05	AC5	SOFTWARE	ASN G:276 , ASN G:279	binding site for Mono-Saccharide NAG G 504 bound to ASN G 276
06	AC6	SOFTWARE	GLU G:269 , ILE G:270 , ASN G:289 , GLN G:344 , LYS G:348	binding site for Mono-Saccharide NAG G 505 bound to ASN G 289
07	AC7	SOFTWARE	ASN G:295 , ASN G:444 , NAG G:502 , HOH G:602	binding site for Mono-Saccharide NAG G 506 bound to ASN G 295
08	AC8	SOFTWARE	LYS G:231 , GLU G:268 , ASN G:334 , LYS G:337	binding site for Mono-Saccharide NAG G 507 bound to ASN G 334
09	AC9	SOFTWARE	MET G:373 , ASN G:386	binding site for Mono-Saccharide NAG G 508 bound to ASN G 386
10	AD1	SOFTWARE	GLN G:389 , ASN G:392	binding site for Mono-Saccharide NAG G 509 bound to ASN G 392
11	AD2	SOFTWARE	ASN G:461	binding site for Mono-Saccharide NAG G 510 bound to ASN G 461

Asymmetric/Biological Unit

No.	Residues
1	G:54	-	G:74
2	G:119	-	G:205
3	G:218	-	G:247
4	G:228	-	G:239
5	G:296	-	G:331
6	G:378	-	G:445
7	G:385	-	G:418
8	G:395	-	G:410
9	H:22	-	H:92
10	H:140	-	H:196
11	L:23	-	L:88
12	L:134	-	L:193
13	N:1	-	N:19
14	N:6	-	N:24
15	N:10	-	N:26

Asymmetric/Biological Unit

No.	Residues
1	Asn G:461	-	Asn G:462
2	Ala H:27	-	Ser H:28
3	Gly H:32	-	Gly H:33
4	Val H:95	-	Pro H:96
5	Phe H:146	-	Pro H:147
6	Glu H:148	-	Pro H:149
7	Val H:211	-	Glu H:212
8	Gly L:28	-	Gly L:29
9	Pro L:40	-	Asp L:41
10	Ser L:93	-	Ser L:94
11	Tyr L:140	-	Pro L:141
12	Gly L:142	-	Ala L:143
13	Ser L:152	-	Ser L:153
14	Lys L:156	-	Ala L:157
15	Ala L:157	-	Gly L:158

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

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

(no "Exon" information available for 5KJR)

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 G from PDB  Type:PROTEIN  Length:332
                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.....eeee.......hhhhhhhh..ee.......eee......eee....hhhhhhhhhhhhhhh....................eeee....eeeeee.......eee...eeee.............ee..........eee..........eeeeeeeeeeeeeee.......eeeehhhhhhhhhhhhhhhhhhhh...eeee......hhhhhheeeee..eeeee.hhhhh...........eee..........................eeeeeeeeeeeeee........eeeeee...hhhhhhhh......eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5kjr G   44 VWKDADTTLFCASDAKAHETEVHNVAATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVISLWDQWLQPCVKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINCTRPSDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITMHSFNCRGEFFYCNTTQLFNNTCIKGCNGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNITGILLTRDGGANNTSNETFRPGGGNIKDNWRSELYKYKVVQIE  492
                                    53        63        73        83        93       103       113      |204       214       224       234       244       254       264       274       284       294     ||328       338       348      |359       369       379       389      |410       420       430       440       450       460       470       480       490  
                                                                                                      120|                                                                                               300|                           355|                                    396|                                                                                    
                                                                                                       202                                                                                                325                            357                                     408

Chain H from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                           
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee...ee.....eeeeee............eeeeee.....eeeeeee.....eee.......eeeeee..eeeeeeee...hhhhheeeeeee..........eee...eeeee........eeeee......eeeeeeeeee....eee.hhhhh....eee...ee.....eeeeeeeee.........ee..eee....eee..ee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5kjr H    1 EVQLVESGPGLVKPSQTLSLTCTVSGASISSGGYFWSWIRQHPGKGLEWIGNIYYIGNTYYNPSLKSRLTISVDTTQNQFSLKLTSVTAADTAVYYCARVPRLRGGNYFDSWGQGTLVTVSSASTKGPSVFPLAPSSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPK  214
                                    10        20        30     || 38        48        58        68        78    ||| 85        95     ||101       111       121      |136       146       156       166       176       186       196       206        
                                                             35A|                                             82A||               100A|||                         128|                                                                                
                                                              35B                                              82B|                100B||                          134                                                                                
                                                                                                                82C                 100C|                                                                                                             
                                                                                                                                     100D

Chain L from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                     
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........ee....eeeeeee...........eeeee.......eeee.............eeeeee..eeeeeee.......eeeeeeee.....eee...eeeee........eeeee..hhhhhh.....eeeeeeee.....eeeeee........eee..........eeeeeee..hhhhhhh...eeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5kjr L    1 QSVLTQPASVSGSPGQSITISCTGTSSDVGGYKYVSWYQQHPDKAPKLMIYEVSNRPSGVSNRFSGSKSGNTASLTISGLQAEDEADYYCSSYTSSSTWVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAP  208
                                    11        21      ||28        38        48        58        68        78        88       |97      106A       116       126       136       146       156       166       176       186       196       206  
                                    9|              27A||                                                                  95A        106A                                                                                                      
                                    11               27B|                                                                                                                                                                                       
                                                      27C

Chain N from PDB  Type:PROTEIN  Length:28
                                                             
               SCOP domains ---------------------------- SCOP domains
               CATH domains ---------------------------- CATH domains
               Pfam domains ---------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh...eeeee..eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------- SAPs(SNPs)
                    PROSITE ---------------------------- PROSITE
                 Transcript ---------------------------- Transcript
                5kjr N    1 xNLHFCQLRCKSLGLLGRCAxTxCACVx   28
                            |       10        20| |    |
                            1-MPT              21-DPR  |
                                                 23-U2X|
                                                      28-NH2

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 '\|'

(no "SCOP Domain" information available for 5KJR)

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

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

Asymmetric/Biological Unit(hide GO term definitions)

(no "Gene Ontology" information available for 5KJR)

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ala H:27 - Ser H:28	[ RasMol ]
		Ala L:157 - Gly L:158	[ RasMol ]
		Asn G:461 - Asn G:462	[ RasMol ]
		Glu H:148 - Pro H:149	[ RasMol ]
		Gly H:32 - Gly H:33	[ RasMol ]
		Gly L:142 - Ala L:143	[ RasMol ]
		Gly L:28 - Gly L:29	[ RasMol ]
		Lys L:156 - Ala L:157	[ RasMol ]
		Phe H:146 - Pro H:147	[ RasMol ]
		Pro L:40 - Asp L:41	[ RasMol ]
		Ser L:152 - Ser L:153	[ RasMol ]
		Ser L:93 - Ser L:94	[ RasMol ]
		Tyr L:140 - Pro L:141	[ RasMol ]
		Val H:211 - Glu H:212	[ RasMol ]
		Val H:95 - Pro H:96	[ RasMol ]

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	5kjr
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4rfo	COMPLEX STRUCTURE WITHOUT GP120 MUTATIONS W69A AND S115W.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 15)

Sites (11, 11)

SS Bonds (15, 15)

Cis Peptide Bonds (15, 15)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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