2VXT: Murine IgG 125-2H

Name: PDB 2VXT: Crystal structure of human IL-18 complexed to murine reference antibody 125-2H Fab
Published: 2009-06-23
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: cytokine

Crystal structure of human IL-18 complexed to murine reference antibody 125-2H Fab. Determined by X-ray diffraction at 1.49 Å resolution. Released 23 Jun 2009.

Method: X-ray diffraction
Resolution: 1.49 Å
Organisms: MUS MUSCULUS, HOMO SAPIENS
Chains: 3
Atoms: 5,375
Mol. weight: 65.09 kDa
Ligands: MG
Released: 23 Jun 2009

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

Secondary structure: helices and β-sheets

2VXT contains 21 α-helices and 58 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 H: 8 helices, 22 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	32	1	3
β-strand	34-40	7	2
β-strand	44-51	8	2
β-strand	57-59	3	2
β-strand	67-72	6	1
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-94	7	2
β-strand	102-103	2	2
β-strand	107-111	5	2
α-helix	114-116	3
β-strand	117	1	4
α-helix	118-119	2
β-strand	120-124	5	5
β-strand	135-145	11	5
β-strand	146	1	4
β-strand	151-154	4	6
α-helix	155-157	3
β-strand	163-165	3	5
α-helix	166-168	3
β-strand	169-170	2	5
β-strand	175-184	10	5
β-strand	194-199	6	6
α-helix	200-202	3
β-strand	204-209	6	6

Chain I: 5 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	38-39	2	7
β-strand	42-49	8	8
α-helix	54	1
β-strand	55-58	4	8
β-strand	64-67	4	8
α-helix	71-76	6
β-strand	83-91	9	8
β-strand	95-103	9	8
β-strand	107-111	5	8
α-helix	113-115	3
β-strand	118-121	4	8
α-helix	123-125	3
β-strand	127-128	2	7
β-strand	137-142	6	8
β-strand	145-153	9	8
β-strand	159-166	8	8
β-strand	169-176	8	8
β-strand	182	1	3
α-helix	183-185	3
β-strand	187-191	5	8

Chain L: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	9
β-strand	10-13	4	2
β-strand	19-25	7	9
β-strand	33-38	6	2
β-strand	44-49	6	2
β-strand	53-54	2	2
α-helix	55	1
β-strand	62-67	6	9
β-strand	70-75	6	9
α-helix	80-82	3
β-strand	85-90	6	2
α-helix	96	1
β-strand	97-98	2	2
β-strand	102-106	5	2
β-strand	111	1	10
α-helix	112-113	2
β-strand	114-118	5	11
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	11
β-strand	140	1	10
β-strand	145-150	6	12
β-strand	153-155	3	12
β-strand	159-163	5	11
α-helix	164-167	4
β-strand	173-182	10	11
α-helix	183-186	4
β-strand	191-197	7	12
β-strand	205-210	6	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Murine IgG 125-2H	H	protein	216	MUS MUSCULUS
Interleukin-18	I	protein	157	HOMO SAPIENS	Q14116 (AlphaFold model)
Murine IgG 125-2H	L	protein	214	MUS MUSCULUS

Sequence of entity 1 (H), FASTA

>2VXT_1 MURINE IGG 125-2H (chains H)
EIQLQQSGPELVKPGASVKVSCKASGYSFTDYFIYWVKQSHGKSLEWIGDIDPYNGDTSY
NQKFRDKATLTVDQSSTTAFMHLNSLTSEDSAVYFCARGLRFWGQGTLVTVSAAKTTPPS
VYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSS
VTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDCG

Sequence of entity 2 (I), FASTA

>2VXT_2 INTERLEUKIN-18 (chains I)
YFGKLESKLSVIRNLNDQVLFIDQGNRPLFEDMTDSDARDNAPRTIFIISMYKDSQPRGM
AVTISVKAEKISTLSAENKIISFKEMNPPDNIKDTKSDIIFFQRSVPGHDNKMQFESSSY
EGYFLAAEKERDLFKLILKKEDELGDRSIMFTVQNED

Sequence of entity 3 (L), FASTA

>2VXT_3 MURINE IGG 125-2H (chains L)
DIQMTQSPSSLSASLGERVSLTCRASQDIGSKLYWLQQEPDGTFKRLIYATSSLDSGVPK
RFSGSRSGSDYSLTISSLESEDFVDYYCLQYASSPYTFGGGTKLAIKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1

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

Primary citation

Unusual Water-Mediated Antigenic Recognition of the Proinflammatory Cytokine Interleukin-18. Argiriadi, M.A., Xiang, T., Wu, C. et al. J Biol Chem (2009) 284:24478. DOI 10.1074/JBC.M109.023887 · PubMed

Other PDB entries of the same protein (UniProt Q14116 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9OD9 1.6 Å, Structure of disulfide-stabilized IL-18 variant
4EKX 1.75 Å, Crystal Structure of YLDV 14L IL-18 Binding Protein in Complex with Human IL-18
7AL7 1.8 Å, The Crystal Structure of Human IL-18 in Complex With Human IL-18 Binding Protein
9OD7 1.9 Å, Structure of disulfide-stabilized IL-18 variant
4XFS 1.91 Å, Structure of IL-18 SER Mutant I
3F62 2.0 Å, Crystal Structure of Human IL-18 in complex with Ectromelia virus IL-18 Binding Protein
4XFT 2.0 Å, Structure of IL-18 SER Mutant III
4HJJ 2.1 Å, Structure Reveals Function of the Dual Variable Domain Immunoglobulin (DVD-Ig) Molecule
3WO2 2.33 Å, Crystal structure of human interleukin-18
4EEE 2.71 Å, Crystal Structure of YLDV 14L IL-18 Binding Protein in Complex with Human IL-18
4R6U 2.8 Å, IL-18 receptor complex
4XFU 2.85 Å, Structure of IL-18 SER Mutant V

Browse structure collections

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