1Q9W: S45-18 Fab pentasaccharide bisphosphate complex

S45-18 Fab pentasaccharide bisphosphate complex. Determined by X-ray diffraction at 1.75 Å resolution. Released 27 Jan 2004.

Method: X-ray diffraction
Resolution: 1.75 Å
Organism: Mus musculus
Chains: 4
Atoms: 7,744
Mol. weight: 99.46 kDa
Ligands: MG
Released: 27 Jan 2004

Explore 1Q9W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1Q9W contains 27 α-helices and 91 β-strands across 4 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: 7 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	1	3
β-strand	31	1	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
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	182-186	5
β-strand	191-196	6	6
α-helix	203	1
β-strand	204-208	5	6

Chain B: 5 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	10-12	3	8
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	34-39	6	8
β-strand	46-51	6	8
β-strand	55-57	3	8
β-strand	62	1	7
β-strand	65-70	6	7
β-strand	75-80	6	7
α-helix	84-86	3
β-strand	88-94	7	8
β-strand	100E-101	2	8
β-strand	105-109	5	8
α-helix	113-114	2
β-strand	115	1	9
β-strand	118-122	5	10
β-strand	133-143	11	10
β-strand	144	1	9
β-strand	149-151	3	11
β-strand	161-163	3	10
α-helix	164-166	3
β-strand	167-169	3	10
β-strand	172-182	11	10
β-strand	192-197	6	11
α-helix	198-200	3
β-strand	202-207	6	11

Chain C: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	12
β-strand	10-14	5	13
β-strand	19-25	7	12
β-strand	30	1	14
β-strand	31	1	14
β-strand	33-38	6	13
β-strand	45-49	5	13
β-strand	53-54	2	13
α-helix	55	1
β-strand	62-67	6	12
β-strand	70-75	6	12
α-helix	80-82	3
β-strand	84-90	7	13
β-strand	96-97	2	13
β-strand	101-106	6	13
β-strand	110	1	15
α-helix	111-112	2
β-strand	113-117	5	16
α-helix	118-120	3
α-helix	121-124	4
β-strand	128-138	11	16
β-strand	139	1	15
β-strand	143-149	7	17
β-strand	152-154	3	17
β-strand	158-162	5	16
α-helix	163-166	4
β-strand	172-181	10	16
α-helix	182-185	4
β-strand	191-197	7	17
α-helix	203	1
β-strand	204-208	5	17

Chain D: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	18
β-strand	10-12	3	19
β-strand	18-25	8	18
α-helix	29-31	3
β-strand	34-39	6	19
β-strand	46-51	6	19
β-strand	55-57	3	19
β-strand	62	1	18
β-strand	65-70	6	18
β-strand	75-80	6	18
α-helix	84-86	3
β-strand	88-94	7	19
β-strand	100E-101	2	19
β-strand	105-109	5	19
α-helix	113-114	2
β-strand	115	1	20
β-strand	118-122	5	21
α-helix	123-125	3
β-strand	134-143	10	21
β-strand	144	1	20
β-strand	149-152	4	22
α-helix	153-155	3
β-strand	157	1	22
β-strand	161-163	3	21
α-helix	164-166	3
β-strand	167-169	3	21
β-strand	172-181	10	21
β-strand	192-197	6	22
α-helix	198-200	3
β-strand	202-207	6	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
S45-18 Fab (IgG1k) light chain	A, C	protein	219	Mus musculus	P01837 (AlphaFold model)
S45-18 Fab (IgG1k) heavy chain	B, D	protein	226	Mus musculus	I6L985 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>1Q9W_1 S45-18 Fab (IgG1k) light chain (chains A, C)
DIVMSQFPSSLAVSAGEKVTMSCKSSQSLLNSRTRKSYLAWYQQKPGQFPKLLIYWAATR
ESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYCKQSYNLRTFGGGTKLEIKRADAAPTV
SIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSM
SSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 2 (B, D), FASTA

>1Q9W_2 S45-18 Fab (IgG1k) heavy chain (chains B, D)
EVILVESGGGLVQPGGSLRLSCSTSGFTFTDYYMSWVRQPPGKALEWLGFIRNKPKGYTT
EYSASVKGRFTISRDNSQSILYLQMNTLRAEDSATYYCVRDIYSFGSRDGMDYWGQGTSV
TVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAV
LQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDC

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	5

Primary citation

Germline antibody recognition of distinct carbohydrate epitopes. Nguyen, H.P., Seto, N.O., MacKenzie, C.R. et al. Nat Struct Biol (2003) 10:1019-1025. DOI 10.1038/nsb1014 · PubMed

Other PDB entries of the same protein (UniProt P01837 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3D9A 1.2 Å, High Resolution Crystal Structure Structure of HyHel10 Fab Complexed to Hen Egg Lysozyme
1RUR 1.5 Å, Crystal Structure (I) of native Diels-Alder antibody 13G5 Fab at pH 8.0 with a data set…
2AJU 1.5 Å, Cyrstal structure of cocaine catalytic antibody 7A1 Fab'
2AJV 1.5 Å, Crystal Structure of Cocaine catalytic Antibody 7A1 Fab' in Complex with Cocaine
2W60 1.5 Å, Anti citrullinated Collagen type 2 antibody acc4
2W9D 1.57 Å, Structure of Fab fragment of the ICSM 18 - anti-Prp therapeutic antibody at 1.57 A…
3BKJ 1.59 Å, Crystal structure of Fab wo2 bound to the n terminal domain of amyloid beta peptide (1-16)
3BAE 1.59 Å, Crystal structure of Fab WO2 bound to the N terminal domain of Amyloid beta peptide (1-28)
2R1Y 1.6 Å, Crystal structure of S25-2 Fab in complex with Kdo analogues
2R2B 1.6 Å, Crystal structure of S25-2 Fab in complex with Kdo analogues
3BKM 1.6 Å, Structure of anti-amyloid-beta Fab WO2 (Form A, P212121)
3CFB 1.6 Å, High-resolution structure of blue fluorescent antibody EP2-19G2 in complex with stilbene…

Browse structure collections

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