8ED1: Bovine Fab 5C1

Bovine Fab 5C1. Determined by X-ray diffraction at 2.31 Å resolution. Released 20 Sept 2023.

Method: X-ray diffraction
Resolution: 2.31 Å
Organisms: Bos taurus, Homo sapiens
Chains: 2
Atoms: 3,626
Mol. weight: 51.89 kDa
Ligands: PO4
Released: 20 Sept 2023

Explore 8ED1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8ED1 contains 19 α-helices and 50 β-strands across 2 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, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	11-12	2	8
β-strand	18-25	8	7
β-strand	34-39	6	9
α-helix	43-44	2
β-strand	45-51	7	9
β-strand	57-59	3	9
α-helix	61-66	6
β-strand	67-72	6	7
β-strand	77-82	6	7
α-helix	84-86	3
β-strand	88-104	17	9
β-strand	109-114	6	10
β-strand	120-128	9	10
α-helix	137-139	3
β-strand	140-141	2	10
α-helix	142-143	2
β-strand	144-156	13	9
β-strand	160-162	3	9
β-strand	163-164	2	8
α-helix	168-169	2
β-strand	170	1	11
β-strand	173-177	5	12
β-strand	185	1	12
β-strand	188-198	11	12
β-strand	199	1	11
β-strand	204-207	4	13
β-strand	217-218	2	12
α-helix	219-221	3
β-strand	222-223	2	12
β-strand	229-238	10	12
β-strand	247-253	7	13
α-helix	254-256	3
β-strand	258-264	7	13
α-helix	265-267	3

Chain L: 10 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	1
β-strand	5	1	2
β-strand	9-14	5	3
β-strand	19-24	6	2
α-helix	28-30	3
β-strand	33-38	6	3
α-helix	43-44	2
β-strand	45-49	5	3
β-strand	53-54	2	3
α-helix	55	1
β-strand	62-67	6	2
β-strand	70-75	6	2
α-helix	80-82	3
β-strand	85-91	7	3
β-strand	96-98	3	3
β-strand	99	1	1
β-strand	102-106A	6	3
α-helix	108-110	3
β-strand	111	1	4
α-helix	112-113	2
β-strand	114-118	5	5
α-helix	119-121	3
α-helix	122-126	5
β-strand	130-139	10	5
β-strand	140	1	4
β-strand	145-150	6	6
β-strand	153-155	3	6
β-strand	159-161	3	5
α-helix	162-164	3
β-strand	165-166	2	5
β-strand	172-180	9	5
α-helix	182-187	6
β-strand	191-197	7	6
β-strand	200-206	7	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
5C1 Fab light chain	L	protein	216	Bos taurus, Homo sapiens	P0DOY2 (AlphaFold model)
5C1 Fab heavy chain	H	protein	272	Bos taurus, Homo sapiens	P0DOX5 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>8ED1_1 5C1 Fab light chain (chains L)
QAVLNQPSSVSGSLGQRVSITCSGSSSNVGNGYVSWYQLIPGSAPRTLIYGDTSRASGVP
DRFSGSRSGNTATLTISSLQAEDEADYFCASAEDSSSNAVFGSGTTLTVLGQPKAAPSVT
LFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASS
YLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 2 (H), FASTA

>8ED1_2 5C1 Fab heavy chain (chains H)
QVQLRESGPSLVKPSQTLSLTCTASGFSLSDKPVGWVRQAPGKPLEWLGSIDTAENTGYN
PGLKSRLSITKDNSKSQVSLSLSSVTTEDSATYYCATVHQKTRKEKSCPDGYLYSSNTGR
GYDCGVWTCRRVGGEFCSATGDWTSPSEEDFYEFYVDTWGQGLLVTVSSASTKGPSVFPL
APSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTV
PSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	1

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

Primary citation

The smallest functional antibody fragment: Ultralong CDR H3 antibody knob regions potently neutralize SARS-CoV-2. Huang, R., Warner Jenkins, G., Kim, Y. et al. Proc Natl Acad Sci U S A (2023) 120:e2303455120-e2303455120. DOI 10.1073/pnas.2303455120 · PubMed

Other PDB entries of the same protein (UniProt P0DOY2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4LLD 1.19 Å, Structure of wild-type IgG1 antibody heavy chain constant domain 1 and light chain…
3TV3 1.29 Å, Crystal structure of broad and potent HIV-1 neutralizing antibody PGT128 in complex with…
4LLQ 1.42 Å, Structure of redesigned IgG1 first constant and lambda domains (CH1:Clambda constant…
4LLY 1.6 Å, Crystal structure of Pertuzumab Clambda Fab with variable and constant domain redesigns…
3TWC 1.65 Å, Crystal structure of broad and potent HIV-1 neutralizing antibody PGT127 in complex with…
4LLM 1.75 Å, Structure of redesigned IgG1 first constant and lambda domains (CH1:Clambda constant…
8ECV 1.81 Å, Bovine Fab 2F12
1AQK 1.84 Å, Three-dimensional structure of a human FAB with high affinity for tetanus toxoid
1JVK 1.94 Å, Three-dimensional structure of an immunoglobulin light chain dimer acting as a lethal…
4LLW 1.95 Å, Crystal structure of Pertuzumab Clambda Fab with variable domain redesign (VRD2) at 1.95A
4EOW 1.97 Å, Crystal structure of a disease-associated anti-human GM-CSF autoantibody MB007
7FAB 2.0 Å, Crystal structure of human immunoglobulin fragment FAB new refined at 2.0 Å resolution

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