1BM3: Immunoglobulin OPG2 FAB-peptide complex

Immunoglobulin OPG2 FAB-peptide complex. Determined by X-ray diffraction at 2.0 Å resolution. Released 20 Apr 1999.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Mus musculus
Chains: 2
Atoms: 3,589
Mol. weight: 48.06 kDa
Released: 20 Apr 1999

Explore 1BM3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1BM3 contains 10 α-helices and 45 β-strands across 2 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, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	6
β-strand	11-12	2	7
β-strand	18-25	8	6
α-helix	29-31	3
β-strand	34-39	6	8
β-strand	45-51	7	8
β-strand	58-59	2	8
β-strand	65	1	9
β-strand	68	1	9
β-strand	69-73	5	6
β-strand	78-83	6	6
α-helix	88-90	3
β-strand	92-95	4	8
β-strand	98	1	8
β-strand	114	1	8
β-strand	119-121	3	8
β-strand	122-123	2	7
β-strand	129	1	10
β-strand	132-136	5	11
β-strand	148-157	10	11
β-strand	158	1	10
β-strand	163-166	4	12
β-strand	176-182	7	11
β-strand	187-195	9	11
β-strand	206-211	6	12
α-helix	212-214	3
β-strand	216-221	6	12

Chain L: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-13	4	2
β-strand	19-25	7	1
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
α-helix	96	1
β-strand	97-98	2	2
β-strand	102-106	5	2
β-strand	111	1	3
β-strand	114-118	5	4
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	4
β-strand	140	1	3
β-strand	145-150	6	5
β-strand	153-155	3	5
β-strand	159-163	5	4
α-helix	165-167	3
β-strand	173-182	10	4
α-helix	183-188	6
β-strand	192-197	6	5
β-strand	205-209	5	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Immunoglobulin OPG2 FAB, constant domain	L	protein	214	Mus musculus
Immunoglobulin OPG2 FAB, variable domain	H	protein	227	Mus musculus	P01868 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>1BM3_1 IMMUNOGLOBULIN OPG2 FAB, CONSTANT DOMAIN (chains L)
DELLTQSPATLSVTPGDSVSLSCRASQSISNNLHWYQQKSHESPRLLIKYASQSISGIPS
RFSGSGSGTDFTLSINSVETEDFGMYFCQQSNSWPLTFGGGSKLEIKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 2 (H), FASTA

>1BM3_2 IMMUNOGLOBULIN OPG2 FAB, VARIABLE DOMAIN (chains H)
EVQLVQSGGGLVNPGRSLKLSCAASGFTFSSYGMSWVRQTPEKRLEWVAAISGGGTYIHY
PDSVKGRFTISRDNAKNNLYLQMSSLRSEDTALYYCTRHPFYRYDGGNYYAMDHWGQGTS
VTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPA
VLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRDC

Primary citation

Conformational change in an anti-integrin antibody: structure of OPG2 Fab bound to a beta 3 peptide. Kodandapani, R., Veerapandian, L., Ni, C.Z. et al. Biochem Biophys Res Commun (1998) 251:61-66. DOI 10.1006/bbrc.1998.9380 · PubMed

Other PDB entries of the same protein (UniProt P01868 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1P7K 1.75 Å, Crystal structure of an anti-ssDNA antigen-binding fragment (Fab) bound to…
1SEQ 1.78 Å, Fab MNAC13
1KEL 1.9 Å, Catalytic antibody 28B4 FAB fragment complexed with hapten…
1R3J 1.9 Å, potassium channel KcsA-Fab complex in high concentration of Tl+
2FD6 1.9 Å, Structure of Human Urokinase Plasminogen Activator in Complex with Urokinase Receptor…
5VJQ 1.9 Å, Complex between HyHEL10 Fab fragment heavy chain mutant (I29F, S52T, Y53F) and Pekin…
1GPO 1.95 Å, Crystal structure of the rationally designed antibody M41 as a FAB fragment
3ZO0 1.99 Å, Mouse IgG2a in complex with mouse TRIM21 PRYSPRY
1FNS 2.0 Å, Crystal structure of the von willebrand factor (VWF) A1 domain I546V mutant in complex…
1OPG 2.0 Å, OPG2 FAB fragment
1P2C 2.0 Å, crystal structure analysis of an anti-lysozyme antibody
1CLO 2.1 Å, Anti-carcinoembryonic antigen monoclonal antibody A5B7

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