6P8M: Antibody P-p3b3 A60C Heavy Chain

Crystal Structure of Antibody P-p3b3 A60C Heavy Chain in Complex with 426c HIV-1 gp120 core G459C. Determined by X-ray diffraction at 3.59 Å resolution. Released 20 Nov 2019.

Method: X-ray diffraction
Resolution: 3.59 Å
Organisms: Human immunodeficiency virus, Mus musculus
Chains: 3
Atoms: 5,868
Mol. weight: 91.21 kDa
Ligands: NAG
Released: 20 Nov 2019

Explore 6P8M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6P8M contains 24 α-helices and 72 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 C: 8 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	53-56	4	1
α-helix	65-73	9
β-strand	74-76	3	1
α-helix	77-78	2
β-strand	84-85	2	2
β-strand	89	1	3
β-strand	91-94	4	4
α-helix	99-115	17
β-strand	120-123	4	5
β-strand	199-202	4	5
β-strand	215	1	6
β-strand	216-218	3	1
β-strand	223-228	6	2
β-strand	236-239	4	4
β-strand	241	1	3
β-strand	242-245	4	2
β-strand	247	1	1
β-strand	251	1	6
β-strand	256	1	7
β-strand	259-261	3	7
α-helix	264-266	3
β-strand	271-273	3	7
β-strand	284-298	15	7
β-strand	329-334	6	7
α-helix	336-353	18
β-strand	358-361	4	7
α-helix	369-372	4
β-strand	373-378	6	7
β-strand	381-386	6	7
β-strand	414-421	8	7
β-strand	423-425	3	5
β-strand	432-434	3	5
α-helix	436-439	4
β-strand	443-456	14	7
β-strand	465-470	6	7
α-helix	476-483	8
β-strand	486-490	5	2

Chain H: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	8
α-helix	7-9	3
β-strand	10-12	3	9
β-strand	17-25	9	8
α-helix	29-31	3
β-strand	34-39	6	9
β-strand	46-51	6	9
β-strand	57-59	3	9
α-helix	61-63	3
β-strand	67-72	6	8
α-helix	73-75	3
β-strand	77-82A	7	8
α-helix	84-86	3
β-strand	88-94	7	9
β-strand	102-103	2	9
β-strand	107-111	5	9
β-strand	117	1	10
β-strand	120	1	11
β-strand	123-124	2	11
β-strand	135-145	11	11
β-strand	146	1	10
β-strand	151-154	4	12
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, 20 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	13
β-strand	10-14	5	14
β-strand	19-24	6	13
β-strand	34-38	5	14
α-helix	43-44	2
β-strand	45-49	5	14
α-helix	54-55	2
β-strand	62-67	6	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	102-107	6	14
β-strand	111	1	15
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	183-188	6
β-strand	192-197	6	17
β-strand	205-209	5	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Gp120	C	protein	347	Human immunodeficiency virus	M4Q8P8
P-p3b3 Heavy Chain	H	protein	233	Mus musculus
P-p3b3 Light Chain	L	protein	216	Mus musculus

Sequence of entity 1 (C), FASTA

>6P8M_1 Gp120 (chains C)
VWKEAKTTLFCASDAKAYEKECHNVWATHACVPTDPNPQEVVLENVTENFNMWKNDMVDQ
MQEDVISIWDQCLKPCVKLTNTSTLTQACPKVTFDPIPIHYCAPAGYAILKCNNKTFNGK
GPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIVIRSKNLRDNAKIIIVQLNKSVEIVC
TRPNNGGSGSGGDIRQAYCNISGRNWSEAVNQVKKKLKEHFPHKNISFQSSSGGDLEITT
HSFNCGGEFFYCNTSGLFNDTISNATIMLPCRIKQIINMWQEVGKAIYAPPIKGNITCKS
DITGLLLLRDGCDTTDNTEIFRPSGGDMRDNWRSELYKYKVVEIKPL

Sequence of entity 2 (H), FASTA

>6P8M_2 P-p3b3 Heavy Chain (chains H)
QVQLVQSGAEVKKPGASVKVSCKASGYTFTGYYIHWVRQAPGQGLEWMGWINPNRGGTNY
CQKFQGRVTMTRDTSISTAYMELSRLRSDDTAVYYCARGINSDYTWDFQHWGQGTLVTVS
SASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQS
SGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTHHHHHH

Sequence of entity 3 (L), FASTA

>6P8M_3 P-p3b3 Light Chain (chains L)
DIVMSQSPSSLAVSVGEKVTMSCKSSQSLLYSSNQKNYLAWYQQKPGQSPKLLIYWASTR
ESGVPDRFTGSGSGTDFTLTISSVKAEDLAVYYCQQYETLGSGTKLEIKRTVAAPSVFIF
PPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSST
LTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	9

Water and common crystallization additives (NA, PEG, EDO, NH4, CL) are not listed.

Primary citation

Overcoming Steric Restrictions of VRC01 HIV-1 Neutralizing Antibodies through Immunization. Parks, K.R., MacCamy, A.J., Trichka, J. et al. Cell Rep (2019) 29:3060-3072.e7. DOI 10.1016/j.celrep.2019.10.071 · PubMed

Other PDB entries of the same protein (UniProt M4Q8P8), best resolution first:

5FA2 2.0 Å, Crystal structure of 426c.TM4deltaV1-3 p120
6MFT 2.31 Å, Crystal structure of glycosylated 426c HIV-1 gp120 core G459C in complex with glVRC01…
6MYY 3.8 Å, Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer, 3 Fabs…
6MZJ 4.8 Å, Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer, 2 Fabs…

Browse structure collections

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