6AL4: Anti-CD19 antibody B43 FAB

Crystal structure of anti-CD19 antibody B43 FAB. Determined by X-ray diffraction at 2.45 Å resolution. Released 28 Mar 2018.

Method: X-ray diffraction
Resolution: 2.45 Å
Organism: Homo sapiens
Chains: 6
Atoms: 10,393
Mol. weight: 147.12 kDa
Released: 28 Mar 2018

Explore 6AL4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6AL4 contains 57 α-helices and 140 β-strands across 6 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
β-strand	4-7	4	1
β-strand	10-13	4	2
β-strand	19-25	7	1
β-strand	30-31	2	3
β-strand	34-35	2	3
β-strand	38-42	5	2
β-strand	49-53	5	2
β-strand	57-58	2	2
α-helix	59	1
β-strand	66-71	6	1
β-strand	74-79	6	1
α-helix	84-86	3
β-strand	89-94	6	2
α-helix	100	1
β-strand	101-102	2	2
β-strand	106-110	5	2
β-strand	115	1	4
α-helix	116-117	2
β-strand	118-122	5	5
α-helix	123-125	3
α-helix	126-130	5
β-strand	133-143	11	5
β-strand	144	1	4
β-strand	149-154	6	6
β-strand	157-158	2	6
α-helix	159	1
β-strand	163-167	5	5
α-helix	168-171	4
β-strand	177-186	10	5
α-helix	187-191	5
β-strand	195-201	7	6
β-strand	209-214	6	6

Chain B: 12 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	7
α-helix	7-9	3
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	46-52	7	8
β-strand	57-60	4	8
α-helix	62-64	3
β-strand	68-73	6	7
α-helix	74-76	3
β-strand	78-83	6	7
α-helix	88-90	3
β-strand	92-99	8	8
α-helix	100-102	3
β-strand	111-114	4	8
β-strand	118-122	5	8
β-strand	128	1	9
α-helix	129-130	2
β-strand	131-135	5	10
β-strand	146-156	11	10
β-strand	157	1	9
β-strand	162-165	4	11
α-helix	166-168	3
β-strand	170	1	11
β-strand	174-176	3	10
α-helix	177-179	3
β-strand	180-181	2	10
β-strand	187-196	10	10
α-helix	197-201	5
β-strand	205-211	7	11
α-helix	212-214	3
β-strand	216-222	7	11
α-helix	224-226	3

Chain C: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	12
β-strand	10-13	4	13
β-strand	19-25	7	12
β-strand	30-31	2	14
β-strand	34-35	2	14
β-strand	38-42	5	13
β-strand	49-53	5	13
β-strand	57-58	2	13
α-helix	59	1
β-strand	66-71	6	12
β-strand	74-79	6	12
α-helix	84-86	3
β-strand	89-94	6	13
α-helix	100	1
β-strand	101-102	2	13
β-strand	106-110	5	13
β-strand	115	1	15
β-strand	116	1	16
α-helix	117	1
β-strand	118-122	5	17
α-helix	123-125	3
α-helix	126-129	4
β-strand	133-143	11	17
β-strand	144	1	15
β-strand	149-154	6	18
β-strand	157-158	2	18
α-helix	159	1
β-strand	163-167	5	17
α-helix	168-171	4
β-strand	177-186	10	17
α-helix	187-191	5
β-strand	195-201	7	18
β-strand	209-214	6	18

Chain D: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	19
β-strand	10-12	3	20
β-strand	18-25	8	19
α-helix	29-31	3
β-strand	34-39	6	20
β-strand	46-52	7	20
β-strand	57-60	4	20
α-helix	62-64	3
β-strand	68-73	6	19
β-strand	78-83	6	19
α-helix	88-90	3
β-strand	92-99	8	20
α-helix	100-102	3
β-strand	111-114	4	20
β-strand	118-122	5	20
α-helix	125-127	3
β-strand	128	1	21
α-helix	129-130	2
β-strand	131-135	5	22
β-strand	142-143	2	22
β-strand	146-156	11	22
β-strand	157	1	21
β-strand	162-165	4	23
α-helix	166-168	3
β-strand	170	1	23
β-strand	174-176	3	22
α-helix	177-179	3
β-strand	180-181	2	22
β-strand	187-196	10	22
α-helix	197-200	4
β-strand	206-211	6	23
α-helix	212-214	3
β-strand	216-221	6	23

Chain E: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	24
β-strand	10-13	4	25
β-strand	19-25	7	24
β-strand	30-31	2	26
β-strand	34-35	2	26
β-strand	38-42	5	25
β-strand	49-53	5	25
β-strand	57-58	2	25
α-helix	59	1
β-strand	66-71	6	24
β-strand	74-79	6	24
α-helix	84-86	3
β-strand	89-94	6	25
α-helix	100	1
β-strand	101-102	2	25
β-strand	103	1	24
β-strand	106-110	5	25
β-strand	115	1	27
α-helix	116-117	2
β-strand	118-122	5	28
α-helix	123-125	3
α-helix	126-129	4
β-strand	133-143	11	28
β-strand	144	1	27
β-strand	149-154	6	16
β-strand	157-158	2	16
α-helix	159	1
β-strand	163-167	5	28
α-helix	168-171	4
β-strand	177-186	10	28
α-helix	187-192	6
β-strand	195-201	7	16
β-strand	209-214	6	16

Chain F: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	29
β-strand	10-12	3	30
β-strand	18-25	8	29
α-helix	29-31	3
β-strand	34-39	6	30
β-strand	45-52	8	30
β-strand	57-60	4	30
α-helix	62-64	3
β-strand	68-73	6	29
β-strand	78-83	6	29
α-helix	88-90	3
β-strand	92-99	8	30
α-helix	100-102	3
β-strand	111-114	4	30
β-strand	118-122	5	30
β-strand	128	1	31
α-helix	129-130	2
β-strand	131-135	5	32
β-strand	143	1	33
β-strand	146	1	33
β-strand	147-156	10	32
β-strand	157	1	31
β-strand	162-165	4	34
α-helix	166-168	3
β-strand	170	1	34
β-strand	174-176	3	32
α-helix	177-179	3
β-strand	180-181	2	32
β-strand	187-195	9	32
β-strand	206-211	6	34
α-helix	212-214	3
β-strand	216-221	6	34

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
B43 light chain	A, C, E	protein	218	Homo sapiens	Q6P5S8 (AlphaFold model)
B43 heavy chain	B, D, F	protein	233	Homo sapiens	Q6GMX6 (AlphaFold model)

Sequence of entity 1 (A, C, E), FASTA

>6AL4_1 B43 LIGHT CHAIN (chains A, C, E)
DIQLTQSPSFLSASVGDRVTITCKASQSVDYSGDSYLNWYQQKPGKAPKLLIYDASNLVS
GVPSRFSGSGSGTEFTLTISSLQPEDFATYYCQQSTENPWTFGGGTKLEIKRTVAAPSVF
IFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS
STLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (B, D, F), FASTA

>6AL4_2 B43 HEAVY CHAIN (chains B, D, F)
QVQLVQSGAEVKKPGSSVKVSCKASGYAFSSYWMNWVRQAPGQGLEWMGQIWPGDSDTNY
AQKFQGRVTITADESTSTAYMELSSLRSEDTAVYYCARRETTTVGRYYYAMDYWGQGTTV
TVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAV
LQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCHHHHHH

Primary citation

Crystal structure of B-cell co-receptor CD19 in complex with antibody B43 reveals an unexpected fold. Teplyakov, A., Obmolova, G., Luo, J. et al. Proteins (2018) 86:495-500. DOI 10.1002/prot.25485 · PubMed

Other PDB entries of the same protein (UniProt Q6P5S8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6UGS 1.95 Å, Crystal structure of the Fab fragment of PF06438179/GP1111 an infliximab biosimilar in a…
2NY1 1.99 Å, HIV-1 gp120 Envelope Glycoprotein (I109C, T257S, S334A, S375W, Q428C) Complexed with CD4…
2NXY 2.0 Å, HIV-1 gp120 Envelope Glycoprotein(S334A) Complexed with CD4 and Antibody 17b
2NY3 2.0 Å, HIV-1 gp120 Envelope Glycoprotein (K231C, T257S, E267C, S334A, S375W) Complexed with CD4…
6UGT 2.15 Å, Crystal structure of the Fab fragment of PF06438179/GP1111 an infliximab biosimilar in a…
6UGU 2.2 Å, Crystal structure of the Fab fragment of anti-TNFa antibody infliximab (Remicade) in a…
6UGV 2.4 Å, Crystal structure of the Fab fragment of anti-TNFa antibody infliximab (Remicade) in a…
2NY6 2.8 Å, HIV-1 gp120 Envelope Glycoprotein (M95W, W96C, I109C, T123C, T257S, V275C,S334A, S375W,…
6V8Z 2.9 Å, VRC03 and 10-1074 Bound BG505 F14 HIV-1 SOSIP Envelope Trimer Structure
6AL5 3.0 Å, Complex between CD19 (N138Q mutant) and B43 FAB
5WKO 3.49 Å, Crystal structure of antibody 27F3 recognizing the HA from A/California/04/2009 (H1N1)…

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