4NPY: Germline PGT121 light chain

Crystal structure of germline Fab PGT121, a putative precursor of the broadly reactive and potent HIV-1 neutralizing antibody. Determined by X-ray diffraction at 1.8 Å resolution. Released 11 Dec 2013.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,302
Mol. weight: 96.72 kDa
Released: 11 Dec 2013

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

Secondary structure: helices and β-sheets

4NPY contains 39 α-helices and 94 β-strands across 4 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: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	14
β-strand	9-13	4	15
β-strand	19-24	6	14
α-helix	28-30	3
β-strand	34-38	5	15
β-strand	45-48	4	15
β-strand	49	1	16
β-strand	53	1	16
α-helix	54-55	2
β-strand	62-67	6	14
β-strand	70-75	6	14
α-helix	80-82	3
β-strand	84-91	8	15
β-strand	96-98	3	15
β-strand	102-106	5	15
α-helix	108-110	3
β-strand	111	1	17
α-helix	112-113	2
β-strand	114-118	5	18
α-helix	119-121	3
α-helix	122-126	5
β-strand	130-139	10	18
β-strand	140	1	17
β-strand	145-150	6	19
β-strand	153-154	2	19
β-strand	159-161	3	18
α-helix	162-164	3
β-strand	165-166	2	18
β-strand	172-180	9	18
α-helix	182-186	5
β-strand	191-197	7	19
β-strand	200-206	7	19

Chain B: 12 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	20
β-strand	11-12	2	21
β-strand	18-25	8	20
β-strand	33-39	7	22
β-strand	46-52	7	22
β-strand	57-59	3	22
α-helix	64-66	3
β-strand	67-72	6	20
α-helix	73-75	3
β-strand	77-82	6	20
α-helix	84-86	3
β-strand	88-100A	14	22
β-strand	100J-103	10	22
β-strand	107-109	3	22
β-strand	110-111	2	21
α-helix	115-116	2
β-strand	117	1	23
α-helix	118-119	2
β-strand	120-124	5	24
α-helix	125-127	3
α-helix	128-130	3
β-strand	135-145	11	24
β-strand	146	1	23
β-strand	151-154	4	25
α-helix	155-157	3
β-strand	159	1	25
β-strand	163-165	3	24
α-helix	166-168	3
β-strand	169-170	2	24
α-helix	171	1
β-strand	176-185	10	24
α-helix	186-188	3
β-strand	195-200	6	25
α-helix	201-203	3
β-strand	205-210	6	25

Chain H: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	8
β-strand	11-12	2	9
β-strand	18-25	8	8
β-strand	33-39	7	10
β-strand	46-52	7	10
β-strand	57-59	3	10
α-helix	64-66	3
β-strand	67-72	6	8
α-helix	73-75	3
β-strand	77-82	6	8
α-helix	84-86	3
β-strand	88-100A	14	10
α-helix	100E-100G	3
β-strand	100J-103	10	10
β-strand	107-109	3	10
β-strand	110-111	2	9
α-helix	115-116	2
β-strand	117	1	11
α-helix	118-119	2
β-strand	120-124	5	12
β-strand	131-132	2	12
β-strand	135-145	11	12
β-strand	146	1	11
β-strand	151-154	4	13
α-helix	155-157	3
β-strand	159	1	13
β-strand	163-165	3	12
α-helix	166-168	3
β-strand	169-170	2	12
β-strand	176-185	10	12
β-strand	195-200	6	13
α-helix	201-203	3
β-strand	205-210	6	13

Chain L: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	1
β-strand	9-13	4	2
β-strand	19-23	5	3
β-strand	24	1	1
α-helix	28-30	3
β-strand	33-38	6	2
β-strand	45-48	4	2
β-strand	49	1	4
β-strand	53	1	4
α-helix	54-55	2
β-strand	62-67	6	3
β-strand	70-75	6	3
α-helix	80-82	3
β-strand	84-91	8	2
β-strand	96-98	3	2
β-strand	102-106	5	2
α-helix	108-110	3
β-strand	111	1	5
α-helix	112-113	2
β-strand	114-118	5	6
α-helix	119-121	3
α-helix	122-126	5
β-strand	130-139	10	6
β-strand	140	1	5
β-strand	145-150	6	7
β-strand	153-155	3	7
β-strand	159-161	3	6
α-helix	162-164	3
β-strand	165-166	2	6
β-strand	172-180	9	6
α-helix	182-187	6
β-strand	191-197	7	7
β-strand	200-206	7	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
germline PGT121 light chain	A, L	protein	215	Homo sapiens	Q6GMX6 (AlphaFold model)
germline PGT121 heavy chain	B, H	protein	235	Homo sapiens	Q6GMX6 (AlphaFold model)

Sequence of entity 1 (A, L), FASTA

>4NPY_1 germline PGT121 light chain (chains A, L)
SYVLTQPPSVSVAPGQTARITCGGNNIGSKSVHWYQQKPGQAPVLVVYDDSDRPSGIPER
FSGSNSGNTATLTISRVEAGDEADYYCQVWDSRGPTNWVFGGGTKLTVLGQPKAAPSVTL
FPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSY
LSLTPEQWKSHKSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 2 (B, H), FASTA

>4NPY_2 germline PGT121 heavy chain (chains B, H)
QVQLQESGPGLVKPSETLSLTCTVSGGSISSYYWSWIRQPPGKGLEWIGYIYYSGSTNYN
PSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARTLHGRRIYGIVAFKEWFTYYYMD
VWGKGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTS
GVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC

Primary citation

The Effects of Somatic Hypermutation on Neutralization and Binding in the PGT121 Family of Broadly Neutralizing HIV Antibodies. Sok, D., Laserson, U., Laserson, J. et al. PLoS Pathog (2013) 9:e1003754-e1003754. DOI 10.1371/journal.ppat.1003754 · PubMed

Other PDB entries of the same protein (UniProt Q6GMX6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5VSI 1.51 Å, CH1/Ckappa Fab mutant 15.1
6DC4 1.7 Å, RSV-neutralizing human antibody AM22
6BAH 1.9 Å, Trastuzumab Fab v3 with 5-diphenyl meditope variant
4LKX 1.92 Å, Humanized antibody 4B12 Fab complexed with a CemX segment
3ZL4 1.95 Å, Antibody structural organization: Role of kappa - lambda chain constant domain switch in…
6B9Y 2.14 Å, Trastuzumab Fab v3 in complex with 5-phenyl meditope variant
5VR9 2.15 Å, CH1/Ckappa Fab based on Matuzumab
6VPY 2.36 Å, I33M (I3.2 mutant from CH103 Lineage)
4FQQ 2.42 Å, Crystal Structure of Germline Antibody PGT121-GL Fab
6AL4 2.45 Å, Crystal structure of anti-CD19 antibody B43 FAB
4D9L 2.48 Å, Fab structure of anti-HIV-1 gp120 V2 mAb 697
5UTZ 2.75 Å, Human IL-2/Fab complex

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