4D9L: Fab structure of anti-HIV-1 gp120 V2 mAb 697

Fab structure of anti-HIV-1 gp120 V2 mAb 697. Determined by X-ray diffraction at 2.48 Å resolution. Released 21 Mar 2012.

Method: X-ray diffraction
Resolution: 2.48 Å
Organism: Homo sapiens
Chains: 8
Atoms: 13,554
Mol. weight: 185.35 kDa
Released: 21 Mar 2012

Explore 4D9L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4D9L contains 62 α-helices and 187 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 H: 10 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	18-25	8	8
α-helix	29-31	3
β-strand	33-39	7	9
β-strand	45-52	8	9
β-strand	56-59	4	9
β-strand	67-72	6	8
β-strand	77-82	6	8
α-helix	84-86	3
β-strand	88-95	8	9
β-strand	102-103	2	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	128-130	3
β-strand	131-132	2	11
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
α-helix	171	1
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 I: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	19
β-strand	10-12	3	20
β-strand	18-25	8	19
α-helix	29-31	3
β-strand	32-39	8	20
β-strand	46-52	7	20
β-strand	56-59	4	20
β-strand	67-72	6	19
β-strand	77-82	6	19
α-helix	84-86	3
β-strand	88-96	9	20
β-strand	102-103	2	20
β-strand	107-111	5	20
α-helix	114-116	3
β-strand	117	1	21
α-helix	118-119	2
β-strand	120-124	5	22
β-strand	135-145	11	22
β-strand	146	1	21
β-strand	151-154	4	23
α-helix	155-157	3
β-strand	159	1	23
β-strand	163-165	3	22
α-helix	166-168	3
β-strand	169-170	2	22
β-strand	176-185	10	22
α-helix	186-188	3
β-strand	195-200	6	23
β-strand	205-210	6	23

Chain J: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	30
α-helix	7-9	3
β-strand	10-12	3	31
β-strand	18-25	8	30
α-helix	29-31	3
β-strand	32-39	8	31
β-strand	46-52	7	31
α-helix	52A-54	3
β-strand	56-59	4	31
β-strand	67-72	6	30
β-strand	77-82	6	30
α-helix	84-86	3
β-strand	88-96	9	31
β-strand	102-103	2	31
β-strand	107-111	5	31
β-strand	117	1	32
α-helix	118-119	2
β-strand	120-124	5	33
α-helix	128-130	3
β-strand	131-132	2	33
β-strand	135-145	11	33
β-strand	146	1	32
β-strand	151-154	4	34
α-helix	155-157	3
β-strand	159	1	34
β-strand	163-165	3	33
α-helix	166-168	3
β-strand	169-170	2	33
β-strand	176-185	10	33
β-strand	195-200	6	34
α-helix	201-203	3
β-strand	205-210	6	34

Chain K: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	41
α-helix	7-9	3
β-strand	10-12	3	42
β-strand	18-25	8	41
α-helix	29-31	3
β-strand	32-39	8	42
β-strand	46-52	7	42
α-helix	52A-54	3
β-strand	56-59	4	42
β-strand	67-72	6	41
β-strand	77-82	6	41
α-helix	84-86	3
β-strand	88-96	9	42
β-strand	102-103	2	42
β-strand	107-111	5	42
β-strand	117	1	43
α-helix	118-119	2
β-strand	120-123	4	44
β-strand	135-145	11	44
β-strand	146	1	43
β-strand	151-154	4	45
α-helix	155-157	3
β-strand	159	1	45
β-strand	163-165	3	44
α-helix	166-168	3
β-strand	169-170	2	44
β-strand	176-185	10	44
β-strand	195-200	6	45
α-helix	201-203	3
β-strand	205-210	6	45

Chain L: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	1
β-strand	5	1	2
β-strand	9-13	4	3
β-strand	18-24	7	2
β-strand	34-38	5	3
β-strand	45-48	4	3
β-strand	49	1	4
β-strand	53	1	4
α-helix	54-55	2
β-strand	62-67	6	2
β-strand	70-76	7	2
α-helix	80-82	3
β-strand	85-92	8	3
β-strand	95B-98	4	3
β-strand	99	1	1
β-strand	102-106	5	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

Chain M: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	13
β-strand	5	1	14
β-strand	9-13	4	13
β-strand	18-24	7	14
β-strand	34-38	5	13
β-strand	45-48	4	13
β-strand	49	1	15
β-strand	53	1	15
α-helix	54-55	2
β-strand	62-67	6	14
β-strand	70-76	7	14
α-helix	80-82	3
β-strand	85-92	8	13
β-strand	95B-99	5	13
β-strand	102-106	5	13
β-strand	111	1	16
α-helix	112-113	2
β-strand	114-118	5	17
α-helix	119-121	3
α-helix	122-125	4
β-strand	130-139	10	17
β-strand	140	1	16
β-strand	145-150	6	18
β-strand	153-155	3	18
β-strand	159-161	3	17
α-helix	162-164	3
β-strand	165-166	2	17
β-strand	172-180	9	17
α-helix	182-187	6
β-strand	191-197	7	18
β-strand	200-206	7	18

Chain N: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	24
β-strand	5	1	25
β-strand	9-13	4	24
β-strand	18-24	7	25
α-helix	27C-29	3
β-strand	34-38	5	24
α-helix	43-44	2
β-strand	45-48	4	24
β-strand	49	1	26
β-strand	53	1	26
β-strand	62-67	6	25
β-strand	70-76	7	25
α-helix	80-82	3
β-strand	84-92	9	24
β-strand	95B-99	5	24
β-strand	102-106	5	24
β-strand	111	1	27
α-helix	112-113	2
β-strand	114-118	5	28
α-helix	119-121	3
α-helix	122-126	5
β-strand	130-139	10	28
β-strand	140	1	27
β-strand	145-150	6	29
β-strand	153-155	3	29
β-strand	159-161	3	28
α-helix	162-164	3
β-strand	165-166	2	28
β-strand	172-180	9	28
α-helix	182-186	5
β-strand	191-197	7	29
β-strand	200-206	7	29

Chain O: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	35
β-strand	5	1	36
β-strand	9-13	4	35
β-strand	19-24	6	36
α-helix	27C-29	3
β-strand	34-38	5	35
β-strand	45-48	4	35
β-strand	49	1	37
β-strand	53	1	37
β-strand	62-67	6	36
β-strand	70-75	6	36
α-helix	80-82	3
β-strand	84-92	9	35
β-strand	95B-99	5	35
β-strand	102-106	5	35
β-strand	111	1	38
α-helix	112-113	2
β-strand	114-118	5	39
α-helix	119-121	3
α-helix	122-126	5
β-strand	130-139	10	39
β-strand	140	1	38
β-strand	145-150	6	40
β-strand	153-154	2	40
β-strand	159-161	3	39
β-strand	165-166	2	39
β-strand	172-180	9	39
α-helix	182-187	6
β-strand	191-197	7	40
β-strand	200-206	7	40

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Light chain of Fab fragment of anti-HIV1 gp120 V2 mAb 697	L, M, N, O	protein	215	Homo sapiens	Q6GMX4 (AlphaFold model)
Heavy chain of Fab fragment of anti-HIV1 gp120 V2 mAb 697	H, I, J, K	protein	223	Homo sapiens	Q6GMX6 (AlphaFold model)

Sequence of entity 1 (L, M, N, O), FASTA

>4D9L_1 Light chain of Fab fragment of anti-HIV1 gp120 V2 mAb 697 (chains L, M, N, O)
QSVLTQPPSVSGAPGQRVTISCTGSSSNIGAHYDVHWYQQLPGTAPKLLIYGNSNRPSGV
PDRFSGSKSGTSASLAITGLQAEDEADYYCQSYDSSLSGYVFGTGTKVTVLGQPKANPTV
TLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAAS
SYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTE

Sequence of entity 2 (H, I, J, K), FASTA

>4D9L_2 Heavy chain of Fab fragment of anti-HIV1 gp120 V2 mAb 697 (chains H, I, J, K)
QVQLVQSGAEVKKPGSSVKVSCKASGGNFNTYTISWVRQAPGQGLEWMGRIIPIFGIVNP
AQKFPGRVTINVDKSTNTAYMELSSLRSEDTAVYYCATSGVGLHFGYFDYWGQGTQVTVS
SASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQS
SGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS

Primary citation

Functional and immunochemical cross-reactivity of V2-specific monoclonal antibodies from HIV-1-infected individuals. Gorny, M.K., Pan, R., Williams, C. et al. Virology (2012) 427:198-207. DOI 10.1016/j.virol.2012.02.003 · PubMed

Other PDB entries of the same protein (UniProt Q6GMX4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5W6C 1.63 Å, UCA Fab (unbound) from 6649 Lineage
6APC 1.7 Å, Crystal Structure of Infant Antibody ADI-19425
5W6G 2.79 Å, Human antibody 6649 in complex with influenza hemagglutinin H1 Solomon Islands
6APD 4.1 Å, Crystal structure of RSV F bound by AM22 and the infant antibody ADI-19425

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