4YDK: PDB entry 4YDK

Crystal structure of broadly and potently neutralizing antibody C38-VRC16.01 in complex with HIV-1 clade AE strain 93TH057 gp120. Determined by X-ray diffraction at 2.05 Å resolution. Released 3 Jun 2015.

Method: X-ray diffraction
Resolution: 2.05 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 3
Atoms: 6,813
Mol. weight: 92.27 kDa
Ligands: NAG, NHE
Released: 3 Jun 2015

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

Secondary structure: helices and β-sheets

4YDK contains 29 α-helices and 73 β-strands across 3 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 G: 12 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	46-47	2	1
β-strand	53-56	4	2
α-helix	65-73	9
β-strand	75-76	2	2
α-helix	77	1
β-strand	84-85	2	1
β-strand	91-94	4	3
α-helix	95-97	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
α-helix	219-220	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	256	1	6
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
β-strand	367	1	7
α-helix	369-372	4
β-strand	374-378	5	6
β-strand	381-385	5	6
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	486-490	5	1

Chain H: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	8
β-strand	10-12	3	9
β-strand	18-25	8	8
α-helix	29-31	3
β-strand	33-39	7	9
β-strand	45-51	7	9
β-strand	57-59	3	9
β-strand	67-72	6	8
β-strand	77-82	6	8
α-helix	84-86	3
β-strand	88-97	10	9
β-strand	100G	1	7
β-strand	100J-103	6	9
β-strand	107-111	5	9
β-strand	117	1	10
α-helix	118-119	2
β-strand	120-124	5	11
α-helix	125-127	3
α-helix	130-131	2
β-strand	135-145	11	11
β-strand	146	1	10
β-strand	151-154	4	12
α-helix	155-157	3
β-strand	159	1	12
β-strand	163-165	3	11
α-helix	166-168	3
β-strand	169-170	2	11
β-strand	176-185	10	11
α-helix	186-188	3
β-strand	195-200	6	12
α-helix	201-203	3
β-strand	205-210	6	12

Chain L: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	13
β-strand	10-13	4	14
β-strand	19-25	7	13
β-strand	33-38	6	14
β-strand	45-49	5	14
β-strand	53-54	2	14
α-helix	55	1
β-strand	62-66	5	13
β-strand	70-75	6	13
α-helix	80-82	3
β-strand	85-90	6	14
β-strand	97-98	2	14
β-strand	102-106	5	14
β-strand	111	1	15
α-helix	112-113	2
β-strand	114-118	5	16
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	16
β-strand	140	1	15
β-strand	145-150	6	17
β-strand	153-154	2	17
α-helix	155	1
β-strand	159-163	5	16
α-helix	164-167	4
β-strand	173-182	10	16
α-helix	183-187	5
β-strand	191-197	7	17
β-strand	205-210	6	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope glycoprotein gp160,Envelope glycoprotein gp160	G	protein	353	Human immunodeficiency virus 1	Q0ED31
Heavy chain of antibody C38-VRC16.01	H	protein	234	Homo sapiens
Light chain of antibody C38-VRC16.01	L	protein	214	Homo sapiens

Sequence of entity 1 (G), FASTA

>4YDK_1 Envelope glycoprotein gp160,Envelope glycoprotein gp160 (chains G)
VWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQ
MQEDVISLWDQSLQPCVKLTGGSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGT
GPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINC
TRPSNGGSGSGGDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITM
HHFNCRGEFFYCNTTQLFNNTCIGNETMKGCNGTITLPCKIKQIINMWQGTGQAMYAPPI
DGKINCVSNITGILLTRDGGANNTSNETFRPGGGNIKDNWRSELYKYKVVQIE

Sequence of entity 2 (H), FASTA

>4YDK_2 HEAVY CHAIN OF ANTIBODY C38-VRC16.01 (chains H)
EVQLSESGGGFVKPGGSLRLSCEASGFTFNNYAMGWVRQAPGKGLEWVSVTSAHGGSAYF
GEFVKGRFTMSRDHFIDTVYLEMNRLTVEDTAVYYCVRVTFYHEGSGYYYRAGNYFDSWG
QGTLVIVSAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVH
TFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDK

Sequence of entity 3 (L), FASTA

>4YDK_3 LIGHT CHAIN OF ANTIBODY C38-VRC16.01 (chains L)
DIQMTQSPSSLSASIGDRVTITCRASQDIANYLNWYQKKSGTPPKLLIFGATNLHHGVSP
RFSGSGHGTHFSLTITNVQHEDFANYFCQQSFQTVGSFGQGTWVDIRRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	10
NHE	2-[N-cyclohexylamino]ethane sulfonic acid	C8 H17 N O3 S	1

Water and common crystallization additives (PEG, GOL) 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
4YDL 1.8 Å, Crystal structure of broadly and potently neutralizing antibody C38-VRC18.02 in complex…
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…
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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