3QCU: LT3015 antibody Fab fragment

Crystal structure of the LT3015 antibody Fab fragment in complex with lysophosphatidic acid (14:0). Determined by X-ray diffraction at 1.98 Å resolution. Released 30 Mar 2011.

Method: X-ray diffraction
Resolution: 1.98 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,020
Mol. weight: 96.52 kDa
Ligands: NKN
Released: 30 Mar 2011

Explore 3QCU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3QCU contains 37 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 H: 9 helices, 23 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	45-51	7	2
β-strand	57-59	3	2
α-helix	61-63	3
β-strand	64	1	1
β-strand	67-72	6	1
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-96	9	2
β-strand	100D-103	5	2
β-strand	107-111	5	2
β-strand	117	1	3
α-helix	118-119	2
β-strand	120-124	5	4
β-strand	135-145	11	4
β-strand	146	1	3
β-strand	151-154	4	5
α-helix	155-157	3
β-strand	159	1	5
β-strand	163-165	3	4
α-helix	166-168	3
β-strand	169-170	2	4
β-strand	176-185	10	4
α-helix	186-190	5
β-strand	195-200	6	5
α-helix	201-203	3
β-strand	205-210	6	5

Chain I: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	12
β-strand	10-12	3	13
β-strand	18-25	8	12
α-helix	29-31	3
α-helix	32-33	2
β-strand	34-39	6	13
β-strand	45-52	8	13
β-strand	56-59	4	13
α-helix	61-63	3
β-strand	67-72	6	12
β-strand	77-82	6	12
α-helix	84-86	3
β-strand	88-96	9	13
β-strand	100D-103	5	13
β-strand	107-111	5	13
β-strand	117	1	14
α-helix	118-119	2
β-strand	120-124	5	15
α-helix	125-127	3
β-strand	135-145	11	15
β-strand	146	1	14
β-strand	151-154	4	16
α-helix	155-157	3
β-strand	159	1	16
β-strand	163-165	3	15
α-helix	166-168	3
β-strand	169-170	2	15
β-strand	176-185	10	15
α-helix	186-188	3
β-strand	195-200	6	16
α-helix	201-203	3
β-strand	205-210	6	16

Chain L: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	6
β-strand	10-13	4	7
β-strand	19-25	7	6
β-strand	27C	1	8
β-strand	31	1	8
β-strand	33-38	6	7
β-strand	45-49	5	7
β-strand	53-54	2	7
α-helix	55	1
β-strand	62-67	6	6
β-strand	70-75	6	6
α-helix	80-82	3
β-strand	84-90	7	7
α-helix	96	1
β-strand	97-98	2	7
β-strand	102-106	5	7
β-strand	111	1	9
α-helix	112-113	2
β-strand	114-118	5	10
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	10
β-strand	140	1	9
β-strand	145-150	6	11
β-strand	153-154	2	11
α-helix	155	1
β-strand	159-163	5	10
α-helix	164-167	4
β-strand	173-182	10	10
α-helix	183-186	4
β-strand	191-197	7	11
β-strand	205-210	6	11

Chain M: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	17
β-strand	10-13	4	18
β-strand	19-25	7	17
β-strand	27C	1	19
β-strand	31	1	19
β-strand	33-38	6	18
β-strand	44-49	6	18
β-strand	53-54	2	18
α-helix	55	1
β-strand	62-67	6	17
β-strand	70-75	6	17
α-helix	80-82	3
β-strand	84-90	7	18
α-helix	96	1
β-strand	97-98	2	18
β-strand	102-106	5	18
β-strand	111	1	20
α-helix	112-113	2
β-strand	114-118	5	21
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	21
β-strand	140	1	20
β-strand	145-150	6	22
β-strand	153-154	2	22
α-helix	155	1
β-strand	159-163	5	21
α-helix	164-167	4
β-strand	173-182	10	21
α-helix	183-187	5
β-strand	191-197	7	22
β-strand	205-210	6	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
LT3015 antibody Fab fragment, heavy chain	H, I	protein	223	Homo sapiens	Q6N089 (AlphaFold model)
LT3015 antibody Fab fragment, light chain	L, M	protein	218	Homo sapiens	P01834 (AlphaFold model)

Sequence of entity 1 (H, I), FASTA

>3QCU_1 LT3015 antibody Fab fragment, heavy chain (chains H, I)
EVQLVQSGAEVKKPGESLKISCQAFGYGFINYLIEWIRQMPGQGLEWIGLINPGSDYTNY
NENFKGQATLSADKSSSTAYLQWSSLKASDTAMYFCARRFGYYGSGNYFDYWGQGTMVTV
SSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPK

Sequence of entity 2 (L, M), FASTA

>3QCU_2 LT3015 antibody Fab fragment, light chain (chains L, M)
DVVMTQTPLSLPVTPGEPASISCTSGQSLVHINGNTYLHWYLQKPGQSPKLLIYKVSNLF
SGVPDRFSGSGSGTDFTLKISRVEAEDVGVYFCSQSTHFPFTFGQGTKLEIKRTVAAPSV
FIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSL
SSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE

Ligands and cofactors

ID	Name	Formula	Copies
NKN	(2R)-2-hydroxy-3-(phosphonooxy)propyl tetradecanoate	C17 H35 O7 P	2

Primary citation

Biochemical and structural characterization of lysophosphatidic Acid binding by a humanized monoclonal antibody. Fleming, J.K., Wojciak, J.M., Campbell, M.A. et al. J Mol Biol (2011) 408:462-476. DOI 10.1016/j.jmb.2011.02.061 · 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
5VKK 2.01 Å, Crystal structure of Fab fragment of anti-CD22 Epratuzumab
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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