6FAX: Lob 7.4 light chain

Complex of Human CD40 Ectodomain with Lob 7.4 Fab. Determined by X-ray diffraction at 2.99 Å resolution. Released 7 Feb 2018.

Method: X-ray diffraction
Resolution: 2.99 Å
Organism: Homo sapiens
Chains: 3
Atoms: 4,084
Mol. weight: 68.52 kDa
Released: 7 Feb 2018

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

Secondary structure: helices and β-sheets

6FAX contains 22 α-helices and 57 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: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	6
β-strand	10-12	3	7
β-strand	18-25	8	6
α-helix	29-31	3
β-strand	32-39	8	7
β-strand	46-52	7	7
β-strand	57-60	4	7
α-helix	62-64	3
β-strand	68-73	6	6
β-strand	78-83	6	6
α-helix	88-90	3
β-strand	92-100	9	7
β-strand	109-112	4	7
β-strand	116-120	5	7
α-helix	124-125	2
β-strand	126	1	8
α-helix	127-128	2
β-strand	129-133	5	9
β-strand	145-154	10	9
β-strand	155	1	8
β-strand	160-163	4	10
α-helix	164-166	3
β-strand	168	1	10
β-strand	173-174	2	9
α-helix	175-177	3
β-strand	178-179	2	9
β-strand	185-193	9	9
α-helix	195-197	3
β-strand	198	1	11
β-strand	201	1	11
β-strand	204-209	6	10
α-helix	210-212	3
β-strand	214-219	6	10

Chain L: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	1
β-strand	10-14	5	2
β-strand	19-25	7	1
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	1
β-strand	70-75	6	1
β-strand	84-90	7	2
α-helix	96	1
β-strand	97-98	2	2
β-strand	102-107	6	2
β-strand	111	1	3
α-helix	112-113	2
β-strand	114-118	5	4
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	4
β-strand	140	1	3
β-strand	145-150	6	5
β-strand	153-154	2	5
α-helix	155-156	2
β-strand	159-163	5	4
α-helix	164-167	4
β-strand	173-182	10	4
α-helix	183-188	6
β-strand	191-197	7	5
β-strand	205-210	6	5

Chain R: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	30-33	4	12
β-strand	36-39	4	12
α-helix	40	1
β-strand	41	1	13
α-helix	42	1
β-strand	45-49	5	14
β-strand	58-61	4	14
β-strand	66-67	2	15
β-strand	72	1	13
α-helix	77	1
β-strand	78-79	2	15
α-helix	80-82	3
α-helix	85-87	3
β-strand	89-93	5	16
β-strand	102-105	4	16
β-strand	111	1	17
β-strand	119	1	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lob 7.4 light chain	L	protein	214	Homo sapiens
Lob 7.4 heavy chain	H	protein	240	Homo sapiens
Tumor necrosis factor receptor superfamily member 5	R	protein	173	Homo sapiens	P25942 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>6FAX_1 Lob 7.4 light chain (chains L)
DIQMTQTTSSLSASLGDRVTITCSASQGINNYLNWYQQKPDGTVKLLIYYTSSLHSGVPS
RFSGSGSGTDYSLTISNLEPEDIATYYCQQYSNLPYTFGGGTKLEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (H), FASTA

>6FAX_2 Lob 7.4 heavy chain (chains H)
EVQLQQSGPDLVKPGASVKISCKTSGYTFTEYIMHWVKQSHGKSLEWIGGIIPNNGGTSY
NQKFKDKATMTVDKSSSTGYMELRSLTSEDSAVYYCTRREVYGRNYYALDYWGQGTLVTV
SSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKCCDKTHTCPPCPAPELL

Sequence of entity 3 (R), FASTA

>6FAX_3 Tumor necrosis factor receptor superfamily member 5 (chains R)
EPPTACREKQYLINSQCCSLCQPGQKLVSDCTEFTETECLPCGESEFLDTWNRETHCHQH
KYCDPNLGLRVQQKGTSETDTICTCEEGWHCTSEACESCVLHRSCSPGFGVKQIATGVSD
TICEPCPVGFFSNVSSAFEKCHPWTSCETKDLVVQQAGTNKTDVVCGPQDRLR

Primary citation

Complex Interplay between Epitope Specificity and Isotype Dictates the Biological Activity of Anti-human CD40 Antibodies. Yu, X., Chan, H.T.C., Orr, C.M. et al. Cancer Cell (2018) 33:664-675.e4. DOI 10.1016/j.ccell.2018.02.009 · PubMed

Other PDB entries of the same protein (UniProt P25942 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1LB6 1.8 Å, TRAF6-CD40 Complex
1D00 2.0 Å, Structure of tnf receptor associated factor 2 in complex with a 5-residue CD40 peptide
7P3I 2.29 Å, Crystal structure of human CD40/TNFRSF5 in complex with the anti-CD40 DARPin protein
1CZZ 2.7 Å, Structure of tnf receptor associated factor 2 in complex with a 17-residue CD40 peptide
8YX1 2.7 Å, CD40 in complex with Bleselumab Fab
5DMJ 2.79 Å, Structure of the extracellular domain of the CD40 in complex with 3H56-5 DAB
8YX9 2.8 Å, CD40 in complex with Dacetuzumab Fab
6PE8 2.84 Å, Crystal structure of CD40/ABBV-323 FAB complex
6PE9 3.13 Å, Crystal Structure of CD40 complexed to FAB516
5IHL 3.3 Å, Structure of the extracellular domain of the CD40 in complex with 3H56-5 dab
1FLL 3.5 Å, Molecular basis for CD40 signaling mediated by TRAF3
3QD6 3.5 Å, Crystal structure of the CD40 and CD154 (CD40L) complex

Browse structure collections

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