2F58: Protein)

IgG1 FAB fragment (58.2) complex with 12-residue cyclic peptide (including residues 315-324 of HIV-1 GP120) (MN isolate). 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: 3,486
Mol. weight: 49.56 kDa
Ligands: ARN
Released: 9 Feb 1999

Explore 2F58 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2F58 contains 14 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: 7 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
α-helix	29-31	3
β-strand	34-39	7	10
β-strand	45-52	8	10
β-strand	57-59	3	10
α-helix	61-64	4
β-strand	67-72	6	8
β-strand	77-82	6	8
α-helix	84-86	3
β-strand	88-99	12	10
β-strand	100E-103	8	10
β-strand	107-109	3	10
β-strand	110-111	2	9
α-helix	115-116	2
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	171-173	3	12
α-helix	174-176	3
β-strand	177-178	2	12
β-strand	185-194	10	12
β-strand	205-212	7	13
α-helix	213-215	3
β-strand	217-223	7	13

Chain L: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	1
β-strand	10-12	3	2
β-strand	19-25	7	1
β-strand	27C-27D	2	3
β-strand	30-31	2	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	84-90	7	2
β-strand	93	1	4
α-helix	96	1
β-strand	97-98	2	2
β-strand	102-105	4	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 (IgG1 FAB 58.2 antibody (light chain))	L	protein	216	Mus musculus	P01666 (AlphaFold model)
Protein (IgG1 FAB 58.2 antibody (heavy chain))	H	protein	228	Mus musculus	P18532 (AlphaFold model)
Protein (HIV-1 GP120)	P	protein	11

Sequence of entity 1 (L), FASTA

>2F58_1 PROTEIN (IGG1 FAB 58.2 ANTIBODY (LIGHT CHAIN)) (chains L)
DIVLTQSPASLAVSLGQRATISCKASQGVDFDGASFMNWYQQKPGQPPKLLIFAASTLES
GIPARFSGRGSGTDFTLNIHPVEEEDAATYYCQQSHEDPLTFGAGTKLELKRADAAPTVS
IFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMS
STLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRA

Sequence of entity 2 (H), FASTA

>2F58_2 PROTEIN (IGG1 FAB 58.2 ANTIBODY (HEAVY CHAIN)) (chains H)
DVQLQQSGPDLVKPSQSLSLTCTVTGYSITSGYSWHWIRQFPGNKLEWMGYIHYSAGTNY
NPSLKSRISITRDTSKNQFFLQLNSVTTEDTATYYCAREEAMPYGNQAYYYAMDCWGQGT
TVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFP
AVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRDC

Sequence of entity 3 (P), FASTA

>2F58_3 PROTEIN (HIV-1 GP120) (chains P)
HIGPGRAFGGG

Ligands and cofactors

ID	Name	Formula	Copies
ARN	1-imino-5-pentanone	C5 H9 N O	1

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…
3F58 2.8 Å, IgG1 FAB fragment (58.2) complex with 12-residue cyclic peptide (including residues…

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