3F58: Protein)

IgG1 FAB fragment (58.2) complex with 12-residue cyclic peptide (including residues 315-324 of HIV-1 GP120 (MN isolate); H315S mutation. Determined by X-ray diffraction at 2.8 Å resolution. Released 9 Feb 1999.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Mus musculus
Chains: 3
Atoms: 3,470
Mol. weight: 49.34 kDa
Released: 9 Feb 1999

Explore 3F58 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3F58 contains 10 α-helices and 47 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 H: 3 helices, 22 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	34-39	7	10
β-strand	45-52	8	10
β-strand	57-59	3	10
β-strand	67-72	6	8
β-strand	77-82	6	8
α-helix	84-86	3
β-strand	88-100	13	10
β-strand	100D-103	9	10
β-strand	107-109	3	10
β-strand	110-111	2	9
β-strand	117	1	11
β-strand	120-124	5	12
β-strand	137-147	11	12
β-strand	148	1	11
β-strand	153-157	4	13
α-helix	162-164	3
β-strand	166	1	13
β-strand	171-178	8	12
β-strand	185-194	10	12
α-helix	198-202	4
β-strand	205-212	7	13
β-strand	217-223	7	13

Chain L: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-14	5	2
β-strand	19-25	7	1
β-strand	27C	1	3
β-strand	31	1	3
β-strand	33-38	6	2
β-strand	45-49	5	2
β-strand	53-54	2	2
α-helix	55	1
β-strand	62-67	6	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	85-90	6	2
β-strand	93	1	4
α-helix	96	1
β-strand	97-98	2	2
β-strand	102-107	6	2
β-strand	111	1	5
β-strand	114-118	5	6
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	6
β-strand	140	1	5
β-strand	144-150	7	7
β-strand	153-154	2	7
β-strand	159-163	5	6
β-strand	173-182	10	6
α-helix	183-186	4
β-strand	191-198	8	7
α-helix	204	1
β-strand	205-210	6	7

Chain P: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	321	1	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein (immunoglobulin gamma I (58.2))	L	protein	215	Mus musculus	P01666 (AlphaFold model)
Protein (immunoglobulin gamma I (58.2))	H	protein	228	Mus musculus	P18532 (AlphaFold model)
Protein (cyclic peptide (GP120))	P	protein	11

Sequence of entity 1 (L), FASTA

>3F58_1 PROTEIN (IMMUNOGLOBULIN GAMMA I (58.2)) (chains L)
DIVLTQSPASLAVSLGQRATISCKASQGVDFDGASFMNWYQQKPGQPPKLLIFAASTLES
GIPARFSGRGSGTDFTLNIHPVEEEDAATYYCQQSHEDPLTFGAGTKLELKRADAAPTVS
IFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMS
STLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR

Sequence of entity 2 (H), FASTA

>3F58_2 PROTEIN (IMMUNOGLOBULIN GAMMA I (58.2)) (chains H)
DVQLQQSGPDLVKPSQSLSLTCTVTGYSITSGYSWHWIRQFPGNKLEWMGYIHYSAGTNY
NPSLKSRISITRDTSKNQFFLQLNSVTTEDTATYYCAREEAMPYGNQAYYYAMDCWGQGT
TVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFP
AVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRDC

Sequence of entity 3 (P), FASTA

>3F58_3 PROTEIN (CYCLIC PEPTIDE (GP120)) (chains P)
SIGPGRAFGGG

Primary citation

Dual conformations for the HIV-1 gp120 V3 loop in complexes with different neutralizing fabs. Stanfield, R., Cabezas, E., Satterthwait, A. et al. Structure (1999) 7:131-142. DOI 10.1016/S0969-2126(99)80020-3 · PubMed

Other PDB entries of the same protein (UniProt P01666 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1F58 2.0 Å, IgG1 FAB fragment (58.2) complex with 24-residue peptide (residues 308-333 of HIV-1…
2F58 2.8 Å, IgG1 FAB fragment (58.2) complex with 12-residue cyclic peptide (including residues…

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