2VQ1: Anti trimeric Lewis X Fab54-5C10-A

anti trimeric Lewis X Fab54-5C10-A. Determined by X-ray diffraction at 2.5 Å resolution. Released 27 Jan 2009.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: MUS MUSCULUS
Chains: 4
Atoms: 6,868
Mol. weight: 95.7 kDa
Ligands: GLY, AZI
Released: 27 Jan 2009

Explore 2VQ1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2VQ1 contains 35 α-helices and 93 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: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-7	4	1
β-strand	10-14	5	2
β-strand	19-25	7	1
β-strand	27C	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
α-helix	96	1
β-strand	97-98	2	2
β-strand	102-107	6	2
β-strand	111	1	4
α-helix	112-113	2
β-strand	114-118	5	5
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	5
β-strand	140	1	4
β-strand	145-150	6	6
β-strand	153-155	3	6
β-strand	159-163	5	5
α-helix	164-167	4
β-strand	173-182	10	5
α-helix	183-188	6
β-strand	192-198	7	6
β-strand	201-209	9	6

Chain B: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	11-12	2	8
α-helix	17	1
β-strand	18-25	8	7
β-strand	34-39	8	9
β-strand	46-52	7	9
β-strand	57-59	3	9
α-helix	64-66	3
β-strand	67-72	6	7
α-helix	73-75	3
β-strand	77-82	6	7
α-helix	84-86	3
β-strand	88-96	9	9
β-strand	103	1	9
β-strand	107-109	3	9
β-strand	110-111	2	8
α-helix	115-116	2
β-strand	117	1	10
α-helix	118-119	2
β-strand	120-124	5	11
β-strand	135-145	11	11
β-strand	146	1	10
β-strand	151-154	4	12
α-helix	155-157	3
β-strand	159	1	12
β-strand	163-165	3	11
α-helix	166-168	3
β-strand	169-171	3	11
β-strand	174-184	11	11
β-strand	194-199	6	12
α-helix	200-202	3
β-strand	204-209	6	12

Chain E: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	13
β-strand	10-14	5	14
β-strand	19-25	7	13
β-strand	27C	1	15
β-strand	31	1	15
β-strand	33-38	6	14
β-strand	45-49	5	14
β-strand	53-54	2	14
α-helix	55	1
β-strand	62-67	6	13
β-strand	70-75	6	13
α-helix	80-82	3
β-strand	84-90	7	14
α-helix	96	1
β-strand	97-98	2	14
β-strand	99	1	13
β-strand	102-107	6	14
β-strand	111	1	16
β-strand	114-118	5	17
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	17
β-strand	140	1	16
β-strand	145-150	6	18
β-strand	153-155	3	18
β-strand	159-163	5	17
α-helix	164-167	4
β-strand	173-182	10	17
α-helix	183-187	5
β-strand	191-197	7	18
β-strand	205-210	6	18

Chain F: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	19
β-strand	11-12	2	20
α-helix	16-17	2
β-strand	18-25	8	19
β-strand	35-39	7	21
β-strand	46-52	7	21
β-strand	57-59	3	21
α-helix	64-66	3
β-strand	67-72	6	19
β-strand	77-82	6	19
α-helix	84-86	3
β-strand	88-95	8	21
α-helix	102	1
β-strand	103	1	21
α-helix	104	1
β-strand	107-109	3	21
β-strand	110-111	2	20
α-helix	115-116	2
β-strand	117	1	22
α-helix	118-119	2
β-strand	120-124	5	23
β-strand	136-143	8	23
β-strand	146	1	22
β-strand	151-154	4	24
α-helix	155-157	3
β-strand	159	1	24
β-strand	163-165	3	23
α-helix	166-168	3
β-strand	169-171	3	23
β-strand	174-183	10	23
β-strand	194-199	6	24
α-helix	200-202	3
β-strand	204-209	6	24

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
IGKV1-117 protein	A, E	protein	217	MUS MUSCULUS	P01631 (AlphaFold model), P01837 (AlphaFold model)
Anti-human fc gamma receptor III 3G8 gamma heavy chain variable region	B, F	protein	218	MUS MUSCULUS	P03987 (AlphaFold model)

Sequence of entity 1 (A, E), FASTA

>2VQ1_1 IGKV1-117 PROTEIN (chains A, E)
DVVMTQTPLSLSVSLGDQASISCRSSQSLVHSNGNTFLQWYLQKPGQSPKLLIYKVSNRF
SGVPDRFSGSGSGTDFTLKISRMEAEDLGIYFCSQTTHVPWTFGGGTKLEIKRADAAPTV
SIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSM
SSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN

Sequence of entity 2 (B, F), FASTA

>2VQ1_2 ANTI-HUMAN FC GAMMA RECEPTOR III 3G8 GAMMA HEAVY CHAIN VARIABLE REGION (chains B, F)
QITLEESGPGILQPSQTLSLTCSFSGFSLSSSAMSVGWIRQPSGKGLEWLAHIWWNDDKY
YNPALKSRLTVSKDSSDNQVFLKIASVVTADTATYYCARIPGFGFDYWGQGTTLTVSSAT
TTAPSVYPLVPGCSDTSGSSVTLGCLVKGYFPEPVTVKWNYGALSSGVRTVSSVLQSGFY
SLSSLVTVPSSTWPSQTVICNVAHPASKTELIKRIEPR

Ligands and cofactors

ID	Name	Formula	Copies
GLY	Glycine	C2 H5 N O2	8
AZI	Azide ion	N3	1

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

Primary citation

Characterization of a Diagnostic Fab Fragment Binding Trimeric Lewis X. De Geus, D.C., Van Roon, A.M.M., Thomassen, E.A.J. et al. Proteins (2009) 76:439. DOI 10.1002/PROT.22356 · PubMed

Other PDB entries of the same protein (UniProt P01631 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1DLF 1.45 Å, High resolution crystal structure of the fv fragment from an anti-dansyl switch variant…
2DLF 1.55 Å, High resolution crystal structure of the fv fragment from an anti-dansyl switch variant…
1N4X 1.7 Å, Structure of scFv 1696 at acidic pH
1WZ1 1.85 Å, Crystal structure of the Fv fragment complexed with dansyl-lysine
1SVZ 1.89 Å, Crystal structure of the single-chain Fv fragment 1696 in complex with the epitope…
2IPT 2.0 Å, PFA1 Fab Fragment
2IQA 2.0 Å, PFA2 FAB fragment, monoclinic apo form
2HKF 2.01 Å, Crystal structure of the Complex Fab M75- Peptide
2O5X 2.05 Å, Crystal structure of 1E9 LeuH47Trp/ArgH100Trp, an engineered Diels-Alderase Fab with nM…
1BFV 2.1 Å, Monoclonal antibody fragment FV4155 from E. Coli
1CFV 2.1 Å, Monoclonal antibody fragment FV4155 from E. Coli
2HKH 2.1 Å, Crystal structure of the Fab M75

Browse structure collections

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