4OQT: LINGO-1/Li81 Fab complex

LINGO-1/Li81 Fab complex. Determined by X-ray diffraction at 3.23 Å resolution. Released 14 May 2014.

Method: X-ray diffraction
Resolution: 3.23 Å
Organism: Homo sapiens
Chains: 3
Atoms: 7,257
Mol. weight: 105.89 kDa
Ligands: NAG
Released: 14 May 2014

Explore 4OQT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4OQT contains 27 α-helices and 87 β-strands across 3 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: 12 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	8-10	3	1
β-strand	15-17	3	1
β-strand	36-38	3	1
β-strand	46-47	2	2
β-strand	60-62	3	1
β-strand	70-71	2	2
β-strand	84-86	3	1
β-strand	108	1	1
β-strand	118-119	2	3
β-strand	132-135	4	1
β-strand	142-143	2	3
β-strand	156-160	5	1
α-helix	169-172	4
β-strand	180-184	5	1
β-strand	190-191	2	4
β-strand	204-208	5	1
β-strand	215-216	2	4
β-strand	228-232	5	1
α-helix	241-244	4
β-strand	252-254	3	1
β-strand	262-263	2	5
α-helix	264	1
β-strand	276-278	3	1
β-strand	286-287	2	5
β-strand	300-302	3	1
α-helix	313-315	3
α-helix	319-321	3
β-strand	324-326	3	1
β-strand	332-333	2	6
α-helix	336-338	3
α-helix	339-343	5
α-helix	345-347	3
β-strand	356	1	7
β-strand	357-359	3	6
α-helix	361-363	3
β-strand	367	1	7
α-helix	368-370	3
α-helix	375-376	2
β-strand	383-387	5	8
β-strand	393-398	6	9
β-strand	403-405	3	10
β-strand	409-412	4	8
β-strand	416	1	11
β-strand	419-420	2	9
β-strand	426-427	2	9
β-strand	435-437	3	10
β-strand	443-445	3	10
α-helix	450-452	3
β-strand	454-459	6	9
β-strand	461	1	11
β-strand	462	1	12
β-strand	465	1	12
β-strand	468-476	9	9

Chain H: 9 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	18
β-strand	10-11	2	19
β-strand	17-25	9	18
β-strand	34-39	6	19
β-strand	45-51	7	19
β-strand	58-60	3	19
β-strand	68-73	6	18
β-strand	78-84	7	18
α-helix	88-90	3
β-strand	92-99	8	19
β-strand	106-108	3	19
β-strand	112-115	4	19
α-helix	119-121	3
β-strand	122	1	20
α-helix	123-124	2
β-strand	125-129	5	21
α-helix	130-132	3
β-strand	140-150	11	21
β-strand	151	1	20
β-strand	155	1	22
β-strand	158-159	2	22
α-helix	160-162	3
β-strand	164	1	22
β-strand	168-170	3	21
α-helix	171-173	3
β-strand	174-175	2	21
β-strand	181-190	10	21
α-helix	191-193	3
β-strand	194	1	23
β-strand	197	1	23
β-strand	199-205	7	22
α-helix	206-208	3
β-strand	210-216	7	22
α-helix	218-220	3

Chain L: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	13
β-strand	10-13	4	14
β-strand	19-25	7	13
β-strand	33-38	6	14
β-strand	45-49	5	14
β-strand	53-54	2	14
β-strand	62-67	6	13
β-strand	70-75	6	13
α-helix	80-82	3
β-strand	84-90	7	14
β-strand	99	1	14
β-strand	103-107	5	14
β-strand	112	1	15
α-helix	113-114	2
β-strand	115-119	5	16
α-helix	120-122	3
α-helix	123-126	4
β-strand	130-140	11	16
β-strand	141	1	15
β-strand	146-151	6	17
β-strand	154-155	2	17
β-strand	160-164	5	16
α-helix	165-168	4
β-strand	174-183	10	16
α-helix	184-187	4
β-strand	192-198	7	17
β-strand	206-211	6	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Leucine-rich repeat and immunoglobulin-like domain-containing nogo receptor-interacting protein 1	A	protein	478	Homo sapiens	Q96FE5 (AlphaFold model)
Light Chain of Li81 Fab, kappa 3	L	protein	215	Homo sapiens	Q6PIL8 (AlphaFold model)
Heavy Chain of Li81 Fab, VH3-23	H	protein	235	Homo sapiens	S6B291 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4OQT_1 Leucine-rich repeat and immunoglobulin-like domain-containing nogo receptor-interacting protein 1 (chains A)
TGCPPRCECSAQDRAVLCHRKRFVAVPEGIPTETRLLDLGKNRIKTLNQDEFASFPHLEE
LELNENIVSAVEPGAFNNLFNLRTLGLRSNRLKLIPLGVFTGLSNLTKLDISENKIVILL
DYMFQDLYNLKSLEVGDNDLVYISHRAFSGLNSLEQLTLEKCNLTSIPTEALSHLHGLIV
LRLRHLNINAIRDYSFKRLYRLKVLEISHWPYLDTMTPNCLYGLNLTSLSITHCNLTAVP
YLAVRHLVYLRFLNLSYNPISTIEGSMLHELLRLQEIQLVGGQLAVVEPYAFRGLNYLRV
LNVSGNQLTTLEESVFHSVGNLETLILDSNPLACDCRLLWVFRRRWRLNFNRQQPTCATP
EFVQGKEFKDFPDVLLPNYFTCRRARIRDRKAQQVFVDEGHTVQFVCRADGDPPPAILWL
SPRKHLVSAKSNGRLTVFPDGTLEVRYAQVQDNGTYLCIAANAGGNDSMPAHLHVRSY

Sequence of entity 2 (L), FASTA

>4OQT_2 Light Chain of Li81 Fab, kappa 3 (chains L)
DIQMTQSPATLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIYDASNRATGIPA
RFSGSGSGTDFTLTISSLEPEDFAVYYCQQRSNWPMYTFGQGTKLEIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (H), FASTA

>4OQT_3 Heavy Chain of Li81 Fab, VH3-23 (chains H)
EVQLLESGGGLVQPGGSLRLSCAASGFTFSAYEMKWVRQAPGKGLEWVSVIGPSGGFTFY
ADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCATEGDNDAFDIWGQGTTVTVSSAS
TKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGL
YSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPEL

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

Primary citation

Structure of the LINGO-1-Anti-LINGO-1 Li81 Antibody Complex Provides Insights into the Biology of LINGO-1 and the Mechanism of Action of the Antibody Therapy. Pepinsky, R.B., Arndt, J.W., Quan, C. et al. J Pharmacol Exp Ther (2014) 350:110-123. DOI 10.1124/jpet.113.211771 · PubMed

Other PDB entries of the same protein (UniProt Q96FE5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2ID5 2.7 Å, Crystal Structure of the Lingo-1 Ectodomain

Browse structure collections

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