3UYR: Monoclonal antibody

Structure of a monoclonal antibody complexed with its MHC-I antigen. Determined by X-ray diffraction at 1.7 Å resolution. Released 25 Jul 2012.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Mus musculus
Chains: 3
Atoms: 3,681
Mol. weight: 48.18 kDa
Released: 25 Jul 2012

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

Secondary structure: helices and β-sheets

3UYR contains 20 α-helices and 44 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: 10 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	1
α-helix	7-8	2
β-strand	10-12	3	2
β-strand	18-24	7	1
α-helix	29-31	3
β-strand	33-40	8	2
β-strand	44-51	8	2
β-strand	58-60	3	2
α-helix	62-64	3
β-strand	68-73	6	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-100	9	2
β-strand	103-107	5	2
β-strand	111-115	5	2
α-helix	119-120	2
β-strand	121	1	3
α-helix	122-123	2
β-strand	124-128	5	4
β-strand	139-149	11	4
β-strand	150	1	3
β-strand	155-158	4	5
α-helix	159-161	3
β-strand	163	1	5
β-strand	167-175	9	4
β-strand	178-188	11	4
α-helix	189-191	3
β-strand	198-203	6	5
α-helix	204-206	3
β-strand	208-213	6	5
α-helix	214	1

Chain L: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	6
β-strand	10-14	5	7
β-strand	19-25	7	6
β-strand	30	1	8
β-strand	36	1	8
β-strand	38-43	6	7
β-strand	49-54	6	7
β-strand	58-59	2	7
α-helix	60	1
β-strand	67-72	6	6
β-strand	75-80	6	6
α-helix	85-87	3
β-strand	89-95	7	7
β-strand	101-102	2	7
β-strand	106-111	6	7
β-strand	115	1	9
α-helix	116-117	2
β-strand	118-122	5	10
α-helix	123-125	3
α-helix	126-129	4
β-strand	133-143	11	10
β-strand	144	1	9
β-strand	149-154	6	11
β-strand	157-158	2	11
β-strand	163-167	5	10
α-helix	168-171	4
β-strand	177-186	10	10
α-helix	187-190	4
β-strand	195-201	7	11
α-helix	208	1
β-strand	209-214	6	11
α-helix	215-217	3

Chain P: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	50-52	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
antibody Fab heavy chain	H	protein	216	Mus musculus
antibody Fab light chain	L	protein	218	Mus musculus	A2NHM3 (AlphaFold model)
H-2 class I histocompatibility antigen, L-D alpha chain	P	protein	8	Mus musculus	P01897 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>3UYR_1 antibody Fab heavy chain (chains H)
EVKLVESEGGLVQPGSSMKLSCTASGFTFSDYYMAWVRQVPEKGLEWVANINYDGSSTYY
LDSLKGRFIISRDIAKNILYLQMSSLRCEDTATYYCARLTNGYLDVWGAGTTVTVSSAKT
TPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLESGLYT
MSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEP

Sequence of entity 2 (L), FASTA

>3UYR_2 antibody Fab light chain (chains L)
DVVMTQTPLSLPVSLGDQASISCRSSQSLVHSNGNTYLHWYLQKPGQSPNLLIYKVSNRF
SGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQSTHVPTFGGGTKLEIKRADAAPTVS
IFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMS
STLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 3 (P), FASTA

>3UYR_3 H-2 class I histocompatibility antigen, L-D alpha chain (chains P)
EPQAPWME

Primary citation

The Peptide-receptive transition state of MHC class I molecules: insight from structure and molecular dynamics. Mage, M.G., Dolan, M.A., Wang, R. et al. J Immunol (2012) 189:1391-1399. DOI 10.4049/jimmunol.1200831 · PubMed

Other PDB entries of the same protein (UniProt A2NHM3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6PXR 1.56 Å, Anti-TAU BIIB092 FAB with TAU peptide
4TPR 1.6 Å, Structure of Tau5 antibody Fab fragment
4TQE 1.6 Å, Structure of tau peptide in complex with Tau5 antibody Fab fragment
3V4U 1.64 Å, Structure of a monoclonal antibody complexed with its MHC-I antigen
3UO1 1.64 Å, Structure of a monoclonal antibody complexed with its MHC-I antigen
2IPU 1.65 Å, PFA1 Fab fragment complexed with Abeta 1-8 peptide
3V52 1.7 Å, Structure of a monoclonal antibody complexed with its MHC-I antigen
2DQU 1.7 Å, Crystal form II: high resolution crystal structure of the complex of the hydrolytic…
1ZEA 1.78 Å, Structure of the anti-cholera toxin antibody Fab fragment TE33 in complex with a D-peptide
1PZ5 1.8 Å, Structural basis of peptide-carbohydrate mimicry in an antibody combining site
2DQT 1.8 Å, High resolution crystal structure of the complex of the hydrolytic antibody Fab 6D9 and…
1T2Q 1.83 Å, The Crystal Structure of an NNA7 Fab that recognizes an N-type blood group antigen

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