6C5J: S25-23 Fab

S25-23 Fab in complex with Chlamydiaceae LPS (Crystal form 1). Determined by X-ray diffraction at 2.29 Å resolution. Released 9 Jan 2019.

Method: X-ray diffraction
Resolution: 2.29 Å
Organism: Mus musculus
Chains: 2
Atoms: 3,456
Mol. weight: 49.04 kDa
Ligands: NAG
Released: 9 Jan 2019

Explore 6C5J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6C5J contains 18 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: 8 helices, 24 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	34-40	7	3
β-strand	44-51	8	3
β-strand	57-59	3	3
α-helix	61-66	6
β-strand	67-72	6	1
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-94	7	3
β-strand	102-103	2	3
β-strand	107-109	3	3
β-strand	110-111	2	2
β-strand	117	1	4
α-helix	118-119	2
β-strand	120-124	5	5
α-helix	128-130	3
β-strand	131-132	2	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
α-helix	187-190	4
β-strand	193-199	7	6
α-helix	200-202	3
β-strand	204-210	7	6

Chain L: 10 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	7
β-strand	10-14	5	3
α-helix	18	1
β-strand	19-25	7	7
β-strand	33-38	6	3
β-strand	45-49	5	3
β-strand	53-54	2	3
α-helix	55	1
β-strand	62-67	6	7
β-strand	70-75	6	7
α-helix	80-82	3
β-strand	85-90	6	3
α-helix	96	1
β-strand	97-98	2	3
β-strand	102-107	6	3
β-strand	111	1	8
α-helix	112-113	2
β-strand	114-118	5	9
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	9
β-strand	140	1	8
β-strand	145-150	6	10
β-strand	153-155	3	10
β-strand	159-163	5	9
α-helix	164-167	4
β-strand	173-182	10	9
α-helix	183-187	5
β-strand	191-197	7	10
α-helix	204	1
β-strand	205-210	6	10

Molecules and chains

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

Sequence of entity 1 (H), FASTA

>6C5J_1 IgG1 Fab Heavy Chain (chains H)
EVQLQESGPGLVQPSQSLSITCTVSGFSLTTYGVHWVRQSPGKGLEWLGVIWSGGTTEYN
AAFISRLSISKDNSKSQVFFKMNSLQTNDTAIYFCVRMRITTDWFAYWGQGTLVTVSAAK
TTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLY
TLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR

Sequence of entity 2 (L), FASTA

>6C5J_2 IgG1 Fab Light Chain (Kappa) (chains L)
DVLMTQTPLSLPVSLGDQASISCRSSQTIVHKNGNTYLEWYLQKPGQSPKLLIYKVSNRF
SGVPDRFSGSGSGTDFTLKISRVEAADLGVYYCFQGSHVPYTFGGGTKLEIKRADAAPTV
SIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSM
SSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

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)
6C5I 1.89 Å, Unliganded S25-5 Fab
6C5H 1.99 Å, S25-5 Fab in complex with Chlamydiaceae-specific LPS antigen
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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