4YDL: PDB entry 4YDL

Crystal structure of broadly and potently neutralizing antibody C38-VRC18.02 in complex with HIV-1 clade AE strain 93TH057gp120. Determined by X-ray diffraction at 1.8 Å resolution. Released 3 Jun 2015.

Method: X-ray diffraction
Resolution: 1.8 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 6
Atoms: 13,805
Mol. weight: 179.44 kDa
Ligands: NAG
Released: 3 Jun 2015

Explore 4YDL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4YDL contains 60 α-helices and 140 β-strands across 6 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: 11 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	45-47	3	17
β-strand	53-56	4	18
α-helix	65-73	9
β-strand	75-76	2	18
α-helix	77-78	2
β-strand	83-86	4	17
β-strand	91-94	4	19
α-helix	99-115	17
β-strand	120-122	3	20
β-strand	200-202	3	20
β-strand	215-218	4	18
β-strand	223-228	6	17
β-strand	236-239	4	19
β-strand	242-245	4	17
β-strand	247	1	18
α-helix	248-250	3
β-strand	251	1	18
β-strand	259-261	3	21
β-strand	271-273	3	21
β-strand	284-298	15	21
β-strand	328-334	7	21
α-helix	335-352	18
α-helix	357	1
β-strand	358-361	4	21
α-helix	369-372	4
β-strand	374-378	5	21
β-strand	381-385	5	21
α-helix	388-390	3
α-helix	393-395	3
β-strand	413-420	8	21
β-strand	423-425	3	20
β-strand	432-434	3	20
α-helix	436-439	4
β-strand	443-456	14	21
β-strand	465-470	6	21
α-helix	476-483	8
β-strand	486-491	6	17

Chain B: 10 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	22
α-helix	7-9	3
β-strand	10-12	3	23
β-strand	18-25	8	22
α-helix	29-31	3
β-strand	34-39	6	23
β-strand	46-52	7	23
β-strand	56-59	4	23
β-strand	68-74	7	22
β-strand	79-82C	7	22
α-helix	84-86	3
β-strand	88-96	9	23
β-strand	99-103	7	23
β-strand	107-111	5	23
β-strand	117	1	24
α-helix	118-119	2
β-strand	120-124	5	25
α-helix	125-127	3
β-strand	135-145	11	25
β-strand	146	1	24
β-strand	151-154	4	26
α-helix	155-157	3
β-strand	159	1	26
β-strand	163-165	3	25
α-helix	166-168	3
β-strand	169-170	2	25
β-strand	176-185	10	25
α-helix	186-188	3
β-strand	189	1	27
β-strand	192	1	27
β-strand	195-200	6	26
α-helix	201-203	3
β-strand	205-210	6	26
α-helix	213-215	3

Chain C: 8 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	28
β-strand	10-13	4	29
β-strand	19-28	11	28
α-helix	30-32	3
β-strand	33-38	6	29
β-strand	45-49	5	29
β-strand	53-54	2	29
α-helix	55	1
β-strand	62-75	14	28
α-helix	80-82	3
β-strand	85-90	6	29
β-strand	97-98	2	29
β-strand	102-106	5	29
β-strand	111	1	30
α-helix	112-113	2
β-strand	114-118	5	31
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	31
β-strand	140	1	30
β-strand	145-150	6	32
β-strand	153-155	3	32
β-strand	159-163	5	31
α-helix	164-167	4
β-strand	173-182	10	31
α-helix	183-186	4
β-strand	191-197	7	32
β-strand	205-210	6	32

Chain G: 11 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	45-47	3	1
β-strand	53-56	4	2
α-helix	65-73	9
β-strand	75-76	2	2
α-helix	77-78	2
β-strand	83-86	4	1
β-strand	91-94	4	3
α-helix	99-115	17
β-strand	120-123	4	4
β-strand	199-202	4	4
β-strand	215	1	5
β-strand	216-218	3	2
β-strand	223-228	6	1
β-strand	236-239	4	3
β-strand	242-245	4	1
β-strand	247	1	2
α-helix	248-250	3
β-strand	251	1	5
β-strand	259-261	3	6
β-strand	271-273	3	6
β-strand	284-298	15	6
β-strand	328-334	7	6
α-helix	335-352	18
α-helix	357	1
β-strand	358-361	4	6
α-helix	369-372	4
β-strand	374-378	5	6
β-strand	381-385	5	6
α-helix	388-390	3
α-helix	393-395	3
β-strand	413-420	8	6
β-strand	423-425	3	4
β-strand	432-434	3	4
α-helix	436-439	4
β-strand	443-456	14	6
β-strand	465-470	6	6
α-helix	476-483	8
β-strand	486-491	6	1

Chain H: 11 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	7
α-helix	7-9	3
β-strand	10-12	3	8
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	34-39	6	8
β-strand	46-52	7	8
β-strand	56-59	4	8
α-helix	61-63	3
β-strand	68-74	7	7
β-strand	79-82C	7	7
α-helix	84-86	3
β-strand	88-96	9	8
β-strand	99-103	7	8
β-strand	107-111	5	8
β-strand	117	1	9
α-helix	118-119	2
β-strand	120-124	5	10
α-helix	125-127	3
β-strand	135-145	11	10
β-strand	146	1	9
β-strand	151-154	4	11
α-helix	155-157	3
β-strand	159	1	11
β-strand	163-165	3	10
α-helix	166-168	3
β-strand	169-170	2	10
β-strand	176-185	10	10
α-helix	186-188	3
β-strand	195-200	6	11
α-helix	201-203	3
β-strand	205-210	6	11
α-helix	213-215	3

Chain L: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-7	4	12
β-strand	10-13	4	13
β-strand	19-25	7	12
α-helix	30-32	3
β-strand	33-38	6	13
β-strand	45-49	5	13
β-strand	53-54	2	13
α-helix	55	1
β-strand	62-67	6	12
β-strand	70-75	6	12
α-helix	80-82	3
β-strand	85-90	6	13
β-strand	97-98	2	13
β-strand	102-106	5	13
β-strand	111	1	14
α-helix	112-113	2
β-strand	114-118	5	15
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	15
β-strand	140	1	14
β-strand	145-150	6	16
β-strand	153-155	3	16
β-strand	159-163	5	15
α-helix	164-167	4
β-strand	173-182	10	15
α-helix	183-186	4
β-strand	191-197	7	16
β-strand	205-210	6	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope glycoprotein gp160,Envelope glycoprotein gp160	A, G	protein	353	Human immunodeficiency virus 1	Q0ED31
Heavy chain of antibody C38-VRC18.02	B, H	protein	226	Homo sapiens
Light chain of antibody C38-VRC18.02	C, L	protein	211	Homo sapiens

Sequence of entity 1 (A, G), FASTA

>4YDL_1 Envelope glycoprotein gp160,Envelope glycoprotein gp160 (chains A, G)
VWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQ
MQEDVISLWDQSLQPCVKLTGGSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGT
GPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINC
TRPSNGGSGSGGDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITM
HHFNCRGEFFYCNTTQLFNNTCIGNETMKGCNGTITLPCKIKQIINMWQGTGQAMYAPPI
DGKINCVSNITGILLTRDGGANNTSNETFRPGGGNIKDNWRSELYKYKVVQIE

Sequence of entity 2 (B, H), FASTA

>4YDL_2 HEAVY CHAIN OF ANTIBODY C38-VRC18.02 (chains B, H)
QVRLVQSGNQVRKPGASVRISCEASGYKFIDHFIHWVRQVPGHGLEWLGWINPRGGGVNY
SRSFQGKLSMTMTRDNFEETAYLDLSKLNPGDTAVYFCARGFAGYEWSFIWGQGTLVIVS
SASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQS
SGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDK

Sequence of entity 3 (C, L), FASTA

>4YDL_3 LIGHT CHAIN OF ANTIBODY C38-VRC18.02 (chains C, L)
EIVLTQSPGTLSLSPGETATLSCRTSQGILSNQLAWHQQRRGQPPRLLIYGGSNRAPGIP
ERFTGSGSGTDFVLTIKRLERDDFAVYYCQILEFFGRGTRVEMNRTVAAPSVFIFPPSDE
QLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSK
ADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	22

Water and common crystallization additives (EPE, SO4) are not listed.

Primary citation

Structural Repertoire of HIV-1-Neutralizing Antibodies Targeting the CD4 Supersite in 14 Donors. Zhou, T., Lynch, R.M., Chen, L. et al. Cell (2015) 161:1280-1292. DOI 10.1016/j.cell.2015.05.007 · PubMed

Other PDB entries of the same protein (UniProt Q0ED31), best resolution first:

4XVT 1.69 Å, Crystal structure of HIV-1 93TH057 coreE gp120 with antibody…
4DKP 1.8 Å, Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with AWS-I-50
4DKR 1.8 Å, Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with AWS-I-169
4H8W 1.85 Å, Crystal structure of non-neutralizing and ADCC-potent antibody N5-i5 in complex with…
4DKQ 1.89 Å, Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with DMJ-I-228
3SE8 1.9 Å, Crystal structure of broadly and potently neutralizing antibody VRC03 in complex with…
3TGT 1.9 Å, Crystal structure of unliganded HIV-1 clade A/E strain 93TH057 gp120 core
4DKO 1.98 Å, Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with TS-II-224
3SE9 2.0 Å, Crystal structure of broadly and potently neutralizing antibody VRC-PG04 in complex with…
4YDK 2.05 Å, Crystal structure of broadly and potently neutralizing antibody C38-VRC16.01 in complex…
4OLZ 2.1 Å, Crystal structure of antibody VRC07-G54W in complex with clade A/E 93TH057 HIV-1 gp120…
4OM1 2.13 Å, Crystal structure of antibody VRC07-I30Q, G54W, S58N in complex with clade A/E 93TH057…

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