5VKK: Fab fragment of anti-CD22 Epratuzumab

Crystal structure of Fab fragment of anti-CD22 Epratuzumab. Determined by X-ray diffraction at 2.01 Å resolution. Released 4 Oct 2017.

Method: X-ray diffraction
Resolution: 2.01 Å
Organisms: Mus musculus, Homo sapiens
Chains: 4
Atoms: 7,184
Mol. weight: 95.59 kDa
Released: 4 Oct 2017

Explore 5VKK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5VKK 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, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	13
α-helix	7-9	3
β-strand	10-12	3	14
β-strand	18-24	7	13
β-strand	33-39	7	14
β-strand	46-52	7	14
β-strand	56-59	4	14
α-helix	61-63	3
β-strand	67-72	6	13
α-helix	73-75	3
β-strand	77-82	6	13
α-helix	84-86	3
β-strand	88-95	8	14
β-strand	101-103	3	14
β-strand	107-111	5	14
β-strand	118	1	15
α-helix	119-120	2
β-strand	121-125	5	16
α-helix	129-131	3
β-strand	132-133	2	16
β-strand	136-146	11	16
β-strand	147	1	15
β-strand	152-155	4	17
α-helix	156-158	3
β-strand	164-166	3	16
α-helix	167-169	3
β-strand	170-171	2	16
β-strand	177-186	10	16
α-helix	187-189	3
β-strand	195-201	7	17
β-strand	206-212	7	17

Chain B: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	18
β-strand	10-14	5	19
β-strand	19-25	7	18
β-strand	27C	1	20
β-strand	31	1	20
β-strand	33-38	6	19
α-helix	43-44	2
β-strand	45-49	5	19
β-strand	53-54	2	19
α-helix	55	1
β-strand	62-67	6	18
β-strand	70-75	6	18
α-helix	80-82	3
β-strand	84-90	7	19
β-strand	97-98	2	19
β-strand	102-107	6	19
β-strand	112	1	21
α-helix	113-114	2
β-strand	115-119	5	22
α-helix	120-122	3
α-helix	123-128	6
β-strand	130-140	11	22
β-strand	141	1	21
β-strand	145-151	7	23
β-strand	154	1	23
β-strand	160-164	5	22
α-helix	165-168	4
β-strand	174-183	10	22
α-helix	184-187	4
β-strand	192-199	8	23
β-strand	206-211	6	23

Chain H: 9 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
α-helix	7-9	3
β-strand	10-12	3	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-39	6	2
β-strand	46-52	7	2
β-strand	56-59	4	2
α-helix	61-63	3
β-strand	67-72	6	1
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-95	8	2
β-strand	101-103	3	2
β-strand	107-111	5	2
β-strand	118	1	3
α-helix	119-120	2
β-strand	121-125	5	4
α-helix	129-131	3
β-strand	132-133	2	4
β-strand	136-146	11	4
β-strand	147	1	3
β-strand	152-155	4	5
α-helix	156-158	3
β-strand	160	1	5
β-strand	164-166	3	4
α-helix	167-169	3
β-strand	170-171	2	4
β-strand	177-186	10	4
α-helix	187-189	3
β-strand	190	1	6
β-strand	193	1	6
β-strand	196-201	6	5
β-strand	206-211	6	5

Chain L: 9 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
α-helix	43-44	2
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
β-strand	97-98	2	8
β-strand	102-106	5	8
β-strand	112	1	10
α-helix	113-114	2
β-strand	115-119	5	11
α-helix	120-122	3
α-helix	123-128	6
β-strand	130-140	11	11
β-strand	141	1	10
β-strand	145-151	7	12
β-strand	154-155	2	12
α-helix	156	1
β-strand	160-164	5	11
α-helix	165-168	4
β-strand	174-183	10	11
α-helix	184-187	4
β-strand	192-199	8	12
β-strand	206-211	6	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Epratuzumab Fab Heavy Chain	A, H	protein	219	Mus musculus, Homo sapiens	Q6N089 (AlphaFold model)
Epratuzumab Fab Light Chain	B, L	protein	219	Mus musculus, Homo sapiens	Q8TCD0 (AlphaFold model)

Sequence of entity 1 (A, H), FASTA

>5VKK_1 Epratuzumab Fab Heavy Chain (chains A, H)
QVQLVQSGAEVKKPGSSVKVSCKASGYTFTSYWLHWVRQAPGQGLEWIGYINPRNDYTEY
NQNFKDKATITADESTNTAYMELSSLRSEDTAFYFCARRDITTFYWGQGTTVTVSSASTK
GPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYS
LSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC

Sequence of entity 2 (B, L), FASTA

>5VKK_2 Epratuzumab Fab Light Chain (chains B, L)
DIQLTQSPSSLSASVGDRVTMSCKSSQSVLYSANHKNYLAWYQQKPGKAPKLLIYWASTR
ESGVPSRFSGSGSGTDFTLTISSLQPEDIATYYCHQYLSSWTFGGGTKLEIKRTVAAPSV
FIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSL
SSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Primary citation

Molecular basis of human CD22 function and therapeutic targeting. Ereno-Orbea, J., Sicard, T., Cui, H. et al. Nat Commun (2017) 8:764-764. DOI 10.1038/s41467-017-00836-6 · PubMed

Other PDB entries of the same protein (UniProt Q6N089 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4HPY 1.5 Å, Crystal structure of RV144-elicited antibody CH59 in complex with V2 peptide
5EWI 1.6 Å, Crystal Structure of the Human Fab VRC38.01, an HIV-1 V1V2-Directed Neutralizing…
4NUJ 1.83 Å, Crystal structure of HIV-1 broadly neutralizing antibody PGT152
3QCU 1.98 Å, Crystal structure of the LT3015 antibody Fab fragment in complex with lysophosphatidic…
3QCT 2.15 Å, Crystal structure of the humanized apo LT3015 anti-lysophosphatidic acid antibody Fab…
3MNV 2.4 Å, Crystal structure of the non-neutralizing HIV antibody 13H11 Fab fragment
3QCV 2.51 Å, Crystal structure of the LT3015 antibody Fab fragment in complex with lysophosphatidic…
5XRQ 2.6 Å, Crystal structure of human monoclonal antibody H3v-47
2OQJ 2.8 Å, Crystal structure analysis of Fab 2G12 in complex with peptide 2G12.1
6V8Z 2.9 Å, VRC03 and 10-1074 Bound BG505 F14 HIV-1 SOSIP Envelope Trimer Structure
5UG0 3.4 Å, Human antibody H2897 in complex with influenza hemagglutinin H1 Solomon Islands/03/2006
5WKO 3.49 Å, Crystal structure of antibody 27F3 recognizing the HA from A/California/04/2009 (H1N1)…

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