4M1D: Anti-HIV-1 Fab 447-52D

Crystal structure of anti-HIV-1 Fab 447-52D in complex with V3 cyclic peptide MN. Determined by X-ray diffraction at 1.8 Å resolution. Released 4 Sept 2013.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 6
Atoms: 8,039
Mol. weight: 99.86 kDa
Released: 4 Sept 2013

Explore 4M1D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4M1D contains 35 α-helices and 100 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 H: 12 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
α-helix	29-31	3
β-strand	34-39	6	10
β-strand	45-51	7	10
α-helix	52B-53	3
β-strand	57-59	3	10
α-helix	61-63	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
β-strand	100F-103	10	10
β-strand	107-109	3	10
β-strand	110-111	2	9
α-helix	114-116	3
β-strand	117	1	11
α-helix	118-119	2
β-strand	120-124	5	12
α-helix	129-131	3
β-strand	135-145	11	12
β-strand	146	1	11
β-strand	151-154	4	13
α-helix	155-157	3
β-strand	163-165	3	12
α-helix	166-168	3
β-strand	169-170	2	12
β-strand	176-185	10	12
α-helix	186-188	3
β-strand	189	1	14
β-strand	192	1	14
β-strand	195-200	6	13
α-helix	201-203	3
β-strand	205-210	6	13

Chain I: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	22
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	45-51	7	23
β-strand	57-59	3	23
β-strand	67-72	6	22
α-helix	73-75	3
β-strand	77-82	6	22
α-helix	84-86	3
β-strand	88-100A	14	23
β-strand	100F-103	10	23
β-strand	107-111	5	23
α-helix	114-116	3
β-strand	117	1	24
α-helix	118-119	2
β-strand	120-124	5	25
β-strand	135-145	11	25
β-strand	146	1	24
β-strand	151-154	4	13
α-helix	155-157	3
β-strand	159	1	13
β-strand	163-165	3	25
α-helix	166-168	3
β-strand	169-170	2	25
β-strand	176-185	10	25
β-strand	195-200	6	13
α-helix	201-203	3
β-strand	205-210	6	13

Chain L: 8 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	19-24	6	2
α-helix	27-29	5
β-strand	34-38	5	3
β-strand	45-48	4	3
β-strand	49	1	4
β-strand	53	1	4
β-strand	62-67	6	2
β-strand	70-75	6	2
α-helix	80-82	3
β-strand	84-91	8	3
β-strand	96-98	3	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
α-helix	208-210	3

Chain M: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	15
β-strand	5	1	16
β-strand	9-13	4	17
β-strand	19-24	6	16
α-helix	27-29	5
β-strand	34-38	5	17
β-strand	45-48	4	17
β-strand	49	1	18
β-strand	53	1	18
β-strand	62-67	6	16
β-strand	70-75	6	16
α-helix	80-82	3
β-strand	84-91	8	17
β-strand	96-98	3	17
β-strand	99	1	15
β-strand	102-106	5	17
β-strand	111	1	19
α-helix	112-113	2
β-strand	114-118	5	20
α-helix	119-121	3
α-helix	122-126	5
β-strand	130-139	10	20
β-strand	140	1	19
β-strand	145-150	6	21
β-strand	153-155	3	21
β-strand	159-161	3	20
α-helix	162-164	3
β-strand	165-166	2	20
β-strand	172-180	9	20
α-helix	182-187	6
β-strand	191-197	7	21
β-strand	200-206	7	21

Chains P and Q: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	306-309	4	10
β-strand	318-319	2	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab mAb 447-52D Light Chain	L, M	protein	216	Homo sapiens	A2NUT2 (AlphaFold model)
Fab mAb 447-52D Heavy Chain	H, I	protein	231	Homo sapiens
Cyclic V3 Arch Peptide	P, Q	protein	14		P05877

Sequence of entity 1 (L, M), FASTA

>4M1D_1 Fab mAb 447-52D Light Chain (chains L, M)
QSVLTQPPSVSAAPGQKVTISCSGSSSNIGNNYVLWYQQFPGTAPKLLIYGNNKRPSGIP
DRFSGSKSGTSATLGITGLQTGDEADYFCATWDSGLSADWVFGGGTKLTVLSQPKAAPSV
TLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAAS
SYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTEC

Sequence of entity 2 (H, I), FASTA

>4M1D_2 Fab mAb 447-52D Heavy Chain (chains H, I)
EVQLVESGGGLVKPGGSLRLTCVASGFTFSDVWLNWVRQAPGKGLEWVGRIKSRTDGGTT
DYAASVKGRFTISRDDSKNTLYLQMNSLKTEDTAVYSCTTDGFIMIRGVSEDYYYYYMDV
WGKGTTVTVSSASTKGPSVFPLAPCSRSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSG
VHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYTCNVNHKPSNTKVDKRVEL

Sequence of entity 3 (P, Q), FASTA

>4M1D_3 Cyclic V3 Arch Peptide (chains P, Q)
CRIHIGPGRAFYTC

Primary citation

Thermodynamic Signatures of the Antigen Binding Site of mAb 447-52D Targeting the Third Variable Region of HIV-1 gp120. Killikelly, A., Zhang, H.T., Spurrier, B. et al. Biochemistry (2013) 52:6249-6257. DOI 10.1021/bi400645e · PubMed

Other PDB entries of the same protein (UniProt A2NUT2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5WKZ 1.85 Å, VH1-69 germline antibody predicted from CR6261
3ZL4 1.95 Å, Antibody structural organization: Role of kappa - lambda chain constant domain switch in…
6VTT 3.7 Å, Cryo-EM Structure of CAP256-VRC26.25 Fab bound to HIV-1 Env trimer CAP256.wk34.c80…

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