2R1X: S25-2 Fab

Crystal structure of S25-2 Fab in complex with Kdo analogues. Determined by X-ray diffraction at 1.6 Å resolution. Released 30 Dec 2008.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Mus musculus
Chains: 2
Atoms: 3,758
Mol. weight: 48.93 kDa
Ligands: MG, ZN
Released: 30 Dec 2008

Explore 2R1X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2R1X contains 18 α-helices and 46 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 A: 9 helices, 23 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	30-30A	2	3
β-strand	30F-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	96-97	2	2
β-strand	101-106	6	2
β-strand	110	1	4
α-helix	111-112	2
β-strand	113-117	5	5
α-helix	118-120	3
α-helix	121-124	4
β-strand	128-138	11	5
β-strand	139	1	4
β-strand	144-149	6	6
β-strand	152-154	3	6
β-strand	158-162	5	5
α-helix	163-166	4
β-strand	172-181	10	5
α-helix	182-185	4
β-strand	190-196	7	6
α-helix	203	1
β-strand	204-209	6	6
α-helix	210-212	3

Chain B: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	11-12	2	8
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	34-39	6	9
β-strand	46-51	6	9
α-helix	52B-52D	3
β-strand	55-57	3	9
β-strand	65-70	6	7
β-strand	75-80	6	7
α-helix	84-86	3
β-strand	88-94	7	9
β-strand	101	1	9
β-strand	105-107	3	9
β-strand	108-109	2	8
α-helix	113-114	2
β-strand	115	1	10
α-helix	116-117	2
β-strand	118-122	5	11
β-strand	133-143	11	11
β-strand	144	1	10
β-strand	149-152	4	12
α-helix	153-155	3
β-strand	157	1	12
β-strand	161-163	3	11
α-helix	164-166	3
β-strand	167-169	3	11
β-strand	172-182	11	11
α-helix	183-185	3
β-strand	192-197	6	12
α-helix	198-200	3
β-strand	202-207	6	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab, antibody fragment (IgG1k), light chain	A	protein	219	Mus musculus	Q52L64 (AlphaFold model)
Fab, antibody fragment (IgG1k), heavy chain	B	protein	222	Mus musculus	A2NU21 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2R1X_1 Fab, antibody fragment (IgG1k), light chain (chains A)
DIVMSQSPSSLAVSAGEKVTMSCKSSQSLLNSRTRKNYLAWYQQKPGQSPKLLIYWASTR
ESGVPDRFTGSGSGTDFTLTITSVQAEDLAVYYCKQSYNLRTFGGGTKLEIKRADAAPTV
SIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSM
SSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 2 (B), FASTA

>2R1X_2 Fab, antibody fragment (IgG1k), heavy chain (chains B)
EVKLVESGGGLVQSGGSLRLSCATSGFTFTDYYMSWVRQPPGKALEWLGFIRNKANGYTT
EYSPSVKGRFTISRDNSQSILYLQMNTLRAEDSATYYCARDHDGYYERFSYWGQGTLVTV
SAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQ
SDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
ZN	Zinc ion	Zn	1

Primary citation

Exploration of specificity in germline monoclonal antibody recognition of a range of natural and synthetic epitopes. Brooks, C.L., Muller-Loennies, S., Brade, L. et al. J Mol Biol (2008) 377:450-468. DOI 10.1016/j.jmb.2008.01.018 · PubMed

Other PDB entries of the same protein (UniProt Q52L64 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3T77 1.74 Å, S25-2- A(2-4)KDO disaccharide complex
1JGU 1.8 Å, Structural basis for disfavored elimination reaction in catalytic antibody 1D4
1JGV 1.85 Å, Structural basis for disfavored elimination reaction in catalytic antibody 1D4
2R2H 2.0 Å, Structure of S25-2 in Complex with Ko
1A3R 2.1 Å, FAB fragment (antibody 8F5) complexed with peptide from human rhinovirus (serotype 2)…
1H3P 2.6 Å, Structural characterisation of a monoclonal antibody specific for the PRES1 region of…
5MP3 2.75 Å, Crystal structure of DC8E8 Fab in the complex with a 30-mer tau peptide at pH 6.5
1BBD 2.8 Å, Three dimensional structure of the FAB fragment of a neutralizing antibody to human…

Browse structure collections

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