2QAD: Tyrosine-sulfated 412d antibody

Structure of tyrosine-sulfated 412d antibody complexed with HIV-1 YU2 gp120 and CD4. Determined by X-ray diffraction at 3.3 Å resolution. Released 25 Sept 2007.

Method: X-ray diffraction
Resolution: 3.3 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 8
Atoms: 14,987
Mol. weight: 216.74 kDa
Ligands: MLA, NAG
Released: 25 Sept 2007

Explore 2QAD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2QAD contains 37 α-helices and 202 β-strands across 8 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 5 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	94	1	1
α-helix	100-115	16
β-strand	120-122	3	2
β-strand	200-202	3	2
β-strand	203	1	3
β-strand	215-217	3	4
β-strand	218	1	5
β-strand	223-228	6	6
β-strand	236	1	1
β-strand	242-245	4	6
β-strand	247	1	5
β-strand	251	1	4
β-strand	256	1	7
β-strand	259-261	3	7
β-strand	271-274	4	7
β-strand	284-298	15	7
β-strand	303-304	2	8
β-strand	307-309	3	9
β-strand	322-322A	2	8
β-strand	328-334	7	7
α-helix	335-353	19
β-strand	359-361	3	7
β-strand	367	1	10
α-helix	369-372	4
β-strand	374-378	5	7
β-strand	381-385	5	7
β-strand	393	1	7
β-strand	413-419	7	7
β-strand	423-425	3	2
β-strand	432-434	3	2
α-helix	436-439	4
β-strand	443-456	14	7
β-strand	466-470	5	7
α-helix	475-480	6
β-strand	486-490	5	6

Chains B and F: 3 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	11
β-strand	12-14	3	12
β-strand	17	1	13
β-strand	27-29	3	11
β-strand	35-38	4	11
β-strand	45	1	10
α-helix	59-64	6
β-strand	66	1	13
β-strand	69-71	3	12
β-strand	81-83	3	11
β-strand	92-98	7	11
β-strand	99-102	4	14
β-strand	107-108	2	15
α-helix	109	1
β-strand	114-119	6	14
β-strand	127	1	16
β-strand	129-130	2	17
β-strand	138-139	2	17
β-strand	143-146	4	14
α-helix	151-153	3
β-strand	155-157	3	18
β-strand	160-162	3	16
β-strand	167-169	3	16
β-strand	172-174	3	18
β-strand	175-176	2	15

Chain C: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
β-strand	5-7	3	19
β-strand	10-13	4	20
β-strand	19-24	6	19
β-strand	34-38	5	20
β-strand	45-49	5	20
β-strand	53-54	2	20
β-strand	62-67	6	19
β-strand	70-75	6	19
β-strand	85-89	5	20
β-strand	93	1	3
α-helix	96-97	2
β-strand	102-106	5	20
α-helix	111-113	3
β-strand	115-118	4	21
α-helix	122-125	4
β-strand	129-130	2	22
β-strand	133-139	7	21
β-strand	146	1	23
β-strand	149	1	24
β-strand	154	1	24
α-helix	155	1
β-strand	160	1	25
β-strand	173-175	3	21
β-strand	178	1	25
β-strand	181-182	2	22
α-helix	184-187	4
β-strand	196	1	23

Chains D and H: 5 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	26
β-strand	10-12	3	27
β-strand	18-20	3	26
β-strand	22-24	3	26
α-helix	29-31	3
β-strand	35-39	5	27
β-strand	45-51	7	27
β-strand	57-59	3	27
α-helix	61-63	3
β-strand	67-72	6	26
β-strand	77-82	6	26
α-helix	84-86	3
β-strand	88-93	6	27
β-strand	94	1	28
β-strand	102	1	28
β-strand	108-111	4	27
β-strand	117	1	29
β-strand	120	1	30
β-strand	138-140	3	31
β-strand	143	1	30
β-strand	146	1	29
β-strand	152-154	3	32
β-strand	164-165	2	31
α-helix	166-168	3
β-strand	169-170	2	30
β-strand	176-177	2	30
β-strand	180-182	3	31
β-strand	195	1	33
β-strand	196-198	3	32
α-helix	201-203	3
β-strand	207	1	32
β-strand	210	1	33

Chain E: 5 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	94	1	34
α-helix	100-115	16
β-strand	120-122	3	35
β-strand	200-202	3	35
β-strand	203	1	36
β-strand	215-217	3	9
β-strand	218	1	37
β-strand	223-228	6	38
β-strand	236	1	34
β-strand	242-245	4	38
β-strand	247	1	37
β-strand	251	1	9
β-strand	256	1	39
β-strand	259-261	3	39
β-strand	271-274	4	39
β-strand	284-298	15	39
β-strand	303-304	2	40
β-strand	307-309	3	4
β-strand	322-322A	2	40
β-strand	328-333	6	39
α-helix	335-353	19
β-strand	359-361	3	39
β-strand	367	1	41
α-helix	369-372	4
β-strand	374-378	5	39
β-strand	381-385	5	39
β-strand	393	1	39
β-strand	414-419	6	39
β-strand	423-425	3	35
β-strand	432-434	3	35
α-helix	436-439	4
β-strand	443-456	14	39
β-strand	466-470	5	39
α-helix	475-480	6
β-strand	486-490	5	38

Chain G: 5 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	50
β-strand	10-13	4	51
β-strand	19-24	6	50
β-strand	34-38	5	51
β-strand	45-49	5	51
β-strand	53-54	2	51
β-strand	62-67	6	50
β-strand	70-75	6	50
β-strand	85-89	5	51
β-strand	93	1	36
α-helix	96-97	2
β-strand	102-106	5	51
α-helix	111-113	3
β-strand	115-118	4	52
α-helix	122-125	4
β-strand	129-130	2	53
β-strand	133-139	7	52
β-strand	146	1	54
β-strand	149	1	55
β-strand	154	1	55
α-helix	155	1
β-strand	160	1	56
β-strand	173-175	3	52
β-strand	178	1	56
β-strand	181-182	2	53
α-helix	184-187	4
β-strand	196	1	54

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope glycoprotein gp160	A, E	protein	322	Human immunodeficiency virus 1	A0A4D7AH25
T-cell surface glycoprotein CD4	B, F	protein	181	Homo sapiens	P01730 (AlphaFold model)
anti-HIV-1 antibody 412d light chain	C, G	protein	214	Homo sapiens	P0DOX7 (AlphaFold model)
anti-HIV-1 antibody 412d heavy chain	D, H	protein	231	Homo sapiens	P01857 (AlphaFold model)

Sequence of entity 1 (A, E), FASTA

>2QAD_1 Envelope glycoprotein gp160 (chains A, E)
VTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTGGSVITQACPKVSFEPIPIHYCAPA
GFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENFTNNA
KTIIVQLNESVVINCTRPNNNTRKSINIGPGRALYTTGEIIGDIRQAHCNLSKTQWENTL
EQIAIKLKEQFGNNKTIIFNPSSGGDPEIVTHSFNCGGEFFYCNSTQLFTWNDTRKLNNT
GRNITLPCRIKQIINMWQEVGKAMYAPPIRGQIRCSSNITGLLLTRDGGKDTNGTEIFRP
GGGDMRDNWRSELYKYKVVKIE

Sequence of entity 2 (B, F), FASTA

>2QAD_2 T-cell surface glycoprotein CD4 (chains B, F)
KKVVLGKKGDTVELTCTASQKKSIQFHWKNSNQIKILGNQGSFLTKGPSKLNDRADSRRS
LWDQGNFPLIIKNLKIEDSDTYICEVEDQKEEVQLLVFGLTANSDTHLLQGQSLTLTLES
PPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCTVLQNQKKVEFKIDIVVLAFQ
K

Sequence of entity 3 (C, G), FASTA

>2QAD_3 anti-HIV-1 antibody 412d light chain (chains C, G)
DIQMTQSPSTLSASVGDRVTITCRASQSISNWLAWYQQKPGRAPKLLMYKASSLKSGVPS
RFSGSGSGTEFTLTISSLQSDDFATYYCQQHDSSPYTFGQGTKLEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKLYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 4 (D, H), FASTA

>2QAD_4 anti-HIV-1 antibody 412d heavy chain (chains D, H)
EVQLVQSGAEVKKPGSSVKVSCKASGGTFSNYAINWVRQAPGQGLEWMGGIIPIFNIAHY
AQRFQGRVSITADESTSTAYMELSSLRSEDTAVFYCASPYPNDYNDYAPEEGMSWYFDLW
GRGTLVTVSPASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGV
HTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

Ligands and cofactors

ID	Name	Formula	Copies
MLA	Malonic acid	C3 H4 O4	4
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	31

Water and common crystallization additives (EDO) are not listed.

Primary citation

Structures of the CCR5 N terminus and of a tyrosine-sulfated antibody with HIV-1 gp120 and CD4. Huang, C.-C., Lam, S.N., Acharya, P. et al. Science (2007) 317:1930-1934. DOI 10.1126/science.1145373 · PubMed

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