5D9Q

Crystal Structure of the BG505 SOSIP gp140 HIV-1 Env trimer in Complex with the Broadly Neutralizing Fab PGT122 and scFv NIH45-46

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	G, A, J	Envelope glycoprotein gp120	polymer	472	52862.8	3	UniProt (Q2N0S6) Pfam (PF00516) In PDB	Human immunodeficiency virus 1
2	B, C, K	Envelope glycoprotein gp41	polymer	152	17031.4	3	UniProt (Q2N0S9) Pfam (PF00517) UniProt (by SIFTS) (Q2N0S6) In PDB	Human immunodeficiency virus 1
3	L, E, M	PGT122 light chain,Ig lambda-3 chain C regions	polymer	211	22712.1	3	UniProt (P0CG06) In PDB	Homo sapiens
4	H, F, N	PGT122 heavy chain,IgG H chain	polymer	235	25448.7	3	UniProt (S6B291) Pfam (PF07686) Pfam (PF07654) In PDB	Homo sapiens
5	D, I, O	NIH45-46 single chain Fv	polymer	241	26304.2	3		Homo sapiens
6	d, f, j, P, R...	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	9	In PDB GlyTouCan (G22768VO)
7	e, Q, s	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	3	In PDB GlyTouCan (G81315DD)
8	a, b, 1, c, 2...	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		424.4	18	In PDB GlyTouCan (G42666HT)
9	h, l, T, v, X...	alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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		1235.1	6	In PDB GlyTouCan (G55220VL)
10	i, U, w	alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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		1883.7	3	In PDB GlyTouCan (G60230HH)
11	0, m, Y	alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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		1721.5	3	In PDB GlyTouCan (G91704UR)
12	G, B, A, C, J...	2-acetamido-2-deoxy-beta-D-glucopyranose	non-polymer		221.2	18	Chemie (NAG)

Sequence modifications

G, A, J: 31 - 504 (UniProt: Q2N0S6)

PDB	External Database	Details
Asn 332	Thr 330	conflict
Ala 460	Ser 457	conflict
Asn 461	Thr 458	conflict
Thr 463	Ser 460	conflict
Ser 464	Thr 461	conflict
Cys 501	Ala 498	conflict

B, C, K: 512 - 663 (UniProt: Q2N0S9)

PDB	External Database	Details
Pro 559	Ile 558	conflict
Cys 605	Thr 604	conflict

L, E, M: 8 - 108 (PDB: 5D9Q)
L, E, M: 109 - 213 (UniProt: P0CG06)

PDB	External Database	Details
Val 156	Ala 49	conflict

H, F, N: 1 - 106 (PDB: 5D9Q)
H, F, N: 107 - 214 (UniProt: S6B291)

Contents of the asymmetric unit

Polymers	Number of chains	15
	Total formula weight	433077.7
Branched	Number of molecules	42
	Total formula weight	36308.9
Non-Polymers*	Number of molecules	18
	Total formula weight	3981.7
All*	Total formula weight	473368.3

*Water molecules are not included.