6C5I: Unliganded S25-5 Fab

Unliganded S25-5 Fab. Determined by X-ray diffraction at 1.89 Å resolution. Released 9 Jan 2019.

Method: X-ray diffraction
Resolution: 1.89 Å
Organism: Mus musculus
Chains: 2
Atoms: 3,713
Mol. weight: 48.31 kDa
Ligands: PG0, NI, NAG
Released: 9 Jan 2019

Explore 6C5I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6C5I contains 16 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 H: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-12	2	2
β-strand	18-25	8	1
β-strand	34-39	6	3
β-strand	45-51	7	3
β-strand	57-59	3	3
β-strand	67-72	6	1
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-93	6	3
β-strand	103	1	3
β-strand	107-109	3	3
β-strand	110-111	2	2
α-helix	114-116	3
β-strand	117	1	4
α-helix	118-119	2
β-strand	120-124	5	5
β-strand	135-145	11	5
β-strand	146	1	4
β-strand	151-154	4	6
α-helix	155-157	3
β-strand	159	1	6
β-strand	163-165	3	5
α-helix	166-168	3
β-strand	169-171	3	5
β-strand	174-184	11	5
β-strand	194-199	6	6
α-helix	200-202	3
β-strand	204-209	6	6

Chain L: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	7
β-strand	10-13	4	8
β-strand	19-25	7	7
β-strand	27C	1	9
β-strand	31	1	9
β-strand	33-38	6	8
β-strand	45-49	5	8
β-strand	53-54	2	8
α-helix	55	1
β-strand	62-67	6	7
β-strand	70-75	6	7
α-helix	80-82	3
β-strand	84-90	7	8
α-helix	96	1
β-strand	97-98	2	8
β-strand	102-106	5	8
β-strand	111	1	10
α-helix	112-113	2
β-strand	114-118	5	11
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	11
β-strand	140	1	10
β-strand	144-150	7	12
β-strand	153-155	3	12
β-strand	159-163	5	11
α-helix	164-167	4
β-strand	173-182	10	11
α-helix	183-187	5
β-strand	191-198	8	12
α-helix	204	1
β-strand	205-210	6	12
α-helix	211-213	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab IgG1 Heavy Chain	H	protein	218	Mus musculus	Q99LC4 (AlphaFold model)
Fab IgG1 (kappa) Light Chain	L	protein	219	Mus musculus	A0A0F7R5U8 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>6C5I_1 Fab IgG1 Heavy Chain (chains H)
EVQLVESGPGLVQPSQSLSITCTVSGFSLSTYGVHWVRQSPGKGLEWLGVIWSGGSTDYN
AAFISRLSITKDNSKSQVFFKMNSLQPNDTAVYYCDRMRITTDWFAYWGQGTLVTVSAAK
TTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLY
TLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR

Sequence of entity 2 (L), FASTA

>6C5I_2 Fab IgG1 (kappa) Light Chain (chains L)
DVLMTQSPLSLPVSLGDQASISCRSSQTIVHSNGNTYLEWYLQKPGQSPKLLIYKVSNRF
YGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPYTFGGGTKLEIKRADAAPTV
SIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSM
SSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Ligands and cofactors

ID	Name	Formula	Copies
PG0	2-(2-methoxyethoxy)ethanol	C5 H12 O3	2
NI	Nickel (II) ion	Ni	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Water and common crystallization additives (CL) are not listed.

Primary citation

Subtle Changes in the Combining Site of the Chlamydiaceae-Specific mAb S25-23 Increase the Antibody-Carbohydrate Binding Affinity by an Order of Magnitude. Haji-Ghassemi, O., Muller-Loennies, S., Brooks, C.L. et al. Biochemistry (2019) 58:714-726. DOI 10.1021/acs.biochem.8b00318 · PubMed

Other PDB entries of the same protein (UniProt Q99LC4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6C5K 1.75 Å, S25-23 Fab in complex with Chlamydiaceae LPS (Crystal form 2)
6C5H 1.99 Å, S25-5 Fab in complex with Chlamydiaceae-specific LPS antigen
6C5J 2.29 Å, S25-23 Fab in complex with Chlamydiaceae LPS (Crystal form 1)
1GIG 2.3 Å, Refined three-dimensional structure of the FAB fragment of a murine IgG1, lambda antibody
3HKF 2.5 Å, Murine unglycosylated IgG Fc fragment
1JHK 2.51 Å, Crystal structure of the anti-estradiol antibody 57-2
2A1W 2.7 Å, Anti-cocaine antibody 7.5.21, crystal form I
5MP3 2.75 Å, Crystal structure of DC8E8 Fab in the complex with a 30-mer tau peptide at pH 6.5
4Q0X 2.9 Å, Crystal structure of non-neutralizing antibody in complex with Epitope II of HCV E2
1JNL 3.0 Å, Crystal Structure of Fab-Estradiol Complexes
1JNN 3.2 Å, Crystal Structure of Fab-Estradiol Complexes
1AFV 3.7 Å, HIV-1 capsid protein (P24) complex with FAB25.3

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