5CEZ

Crystal Structure of the BG505 SOSIP gp140 HIV-1 Env trimer in Complex with an early putative precursor of the PGT121 family at 3.0 Angstrom

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	G	Envelope glycoprotein gp160	polymer	480	53950.2	1	UniProt (Q2N0S6) Pfam (PF00516) In PDB	Human immunodeficiency virus 1	Endogenous retrovirus group K member 113 Env polyprotein,Endogenous retrovirus group K member 13-1 Env polyprotein,Endogenous retrovirus group K member 18 Env polyprotein,Endogenous retrovirus group K member 19 Env polyprotein,Endogenous retrovirus group K member 21 Env polyprotein,Endogenous retrovirus group K member 24 Env polyprotein,Endogenous retrovirus group K member 25 Env polyprotein,Endogenous retrovirus group K member 6 Env polyprotein,Endogenous retrovirus group K member 7 Env polyprotein,Endogenous retrovirus group K member 8 Env polyprotein,Endogenous retrovirus group K member 9 Env polyprotein,Envelope glycoprotein gp160
2	B	Envelope glycoprotein gp160	polymer	153	17146.5	1	UniProt (Q2N0S6) Pfam (PF00517) In PDB	Human immunodeficiency virus 1	Endogenous retrovirus group K member 113 Env polyprotein,Endogenous retrovirus group K member 13-1 Env polyprotein,Endogenous retrovirus group K member 18 Env polyprotein,Endogenous retrovirus group K member 19 Env polyprotein,Endogenous retrovirus group K member 21 Env polyprotein,Endogenous retrovirus group K member 24 Env polyprotein,Endogenous retrovirus group K member 25 Env polyprotein,Endogenous retrovirus group K member 6 Env polyprotein,Endogenous retrovirus group K member 7 Env polyprotein,Endogenous retrovirus group K member 8 Env polyprotein,Endogenous retrovirus group K member 9 Env polyprotein,Envelope glycoprotein gp160
3	L	3H+109L Fab Light Chain	polymer	218	23427.0	1		Homo sapiens
4	H	3H+109L Fab Heavy Chain	polymer	236	25339.4	1		Homo sapiens
5	D	35022 Fab Heavy Chain	polymer	240	25783.1	1		Homo sapiens
6	E	35022 Fab Light Chain	polymer	216	23318.8	1		Homo sapiens
7	A	alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		1235.1	1	In PDB GlyTouCan (G46836GH)
8	C, F, I, J, K...	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		424.4	6	In PDB GlyTouCan (G42666HT)
9	N	alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		910.8	1	In PDB GlyTouCan (G22768VO)
10	O	alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		748.7	1	In PDB GlyTouCan (G81315DD)
11	P	alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		1073.0	1	In PDB GlyTouCan (G09724ZC)
12	Q	alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		1559.4	1	In PDB GlyTouCan (G04414GO)
13	G, B	2-acetamido-2-deoxy-beta-D-glucopyranose	non-polymer		221.2	6	Chemie (NAG)
14	H, D	alpha-D-mannopyranose	non-polymer		180.2	2	Chemie (MAN)

Sequence modifications

G: 32 - 511 (UniProt: Q2N0S6)

PDB	External Database	Details
Ala 137	Asn 136	engineered mutation
Asn 332	Thr 330	engineered mutation
Cys 501	Ala 498	engineered mutation
Arg 509	Glu 506	insertion
Arg 510	Lys 507	insertion
Arg 512	-	insertion
Arg 513	-	insertion

B: 512 - 664 (UniProt: Q2N0S6)

PDB	External Database	Details
Pro 559	Ile 556	engineered mutation
Cys 605	Thr 602	engineered mutation

Contents of the asymmetric unit

Polymers	Number of chains	6
	Total formula weight	168964.9
Branched	Number of molecules	11
	Total formula weight	8073.4
Non-Polymers*	Number of molecules	8
	Total formula weight	1687.6
All*	Total formula weight	178725.9

*Water molecules are not included.