8P6I: 139H2 Fab fragment

Crystal structure of the 139H2 Fab fragment bound to Muc1 peptide epitope. Determined by X-ray diffraction at 2.5 Å resolution. Released 3 Apr 2024.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 6
Atoms: 6,948
Mol. weight: 101.63 kDa
Released: 3 Apr 2024

Explore 8P6I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8P6I contains 34 α-helices and 89 β-strands across 6 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: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3

Chain A: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3

Chain h: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	12
β-strand	10-12	3	13
β-strand	18-25	8	12
α-helix	29-31	3
β-strand	34-39	6	13
β-strand	46-51	6	13
β-strand	58-60	3	13
α-helix	62-64	3
β-strand	68-73	6	12
α-helix	74-76	3
β-strand	78-83	6	12
α-helix	88-90	3
β-strand	92-102	11	13
β-strand	105-112	8	13
β-strand	116-120	5	13
β-strand	126	1	14
α-helix	127-128	2
β-strand	129-133	5	15
β-strand	144-154	11	15
β-strand	155	1	14
β-strand	160-164	5	16
β-strand	171-174	4	15
α-helix	175-177	3
β-strand	178-180	3	15
β-strand	183-193	11	15
β-strand	203-208	6	16
α-helix	209-211	3
β-strand	213-218	6	16

Chain H: 9 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	34-39	6	2
β-strand	46-51	6	2
β-strand	58-60	3	2
α-helix	62-64	3
β-strand	68-73	6	1
α-helix	74-76	3
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-102	11	2
β-strand	105-112	8	2
β-strand	116-120	5	2
β-strand	126	1	3
α-helix	127-128	2
β-strand	129-133	5	4
β-strand	144-154	11	4
β-strand	155	1	3
β-strand	160-163	4	5
α-helix	164-166	3
β-strand	168	1	5
β-strand	172-174	3	4
α-helix	175-177	3
β-strand	178-180	3	4
β-strand	183-193	11	4
β-strand	202-208	7	5
α-helix	209-211	3
β-strand	213-219	7	5

Chain l: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	17
β-strand	10-13	4	18
β-strand	19-25	7	17
β-strand	30	1	19
β-strand	37	1	19
β-strand	39-44	6	18
β-strand	51-55	5	18
β-strand	59-60	2	18
α-helix	61	1
β-strand	68-73	6	17
β-strand	76-81	6	17
α-helix	86-88	3
β-strand	91-96	6	18
α-helix	102	1
β-strand	103-104	2	18
β-strand	108-112	5	18
β-strand	117	1	20
α-helix	118-119	2
β-strand	120-124	5	21
α-helix	125-127	3
α-helix	128-133	6
β-strand	135-145	11	21
β-strand	146	1	20
β-strand	151-156	6	22
β-strand	159-161	3	22
β-strand	165-169	5	21
α-helix	170-173	4
β-strand	179-188	10	21
α-helix	189-193	5
β-strand	197-203	7	22
β-strand	211-216	6	22

Chain L: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	6
β-strand	10-13	4	7
β-strand	19-25	7	6
β-strand	30-31	2	8
β-strand	36-37	2	8
β-strand	39-44	6	7
β-strand	51-55	5	7
β-strand	59-60	2	7
α-helix	61	1
β-strand	68-73	6	6
β-strand	76-81	6	6
α-helix	86-88	3
β-strand	91-96	6	7
α-helix	102	1
β-strand	103-104	2	7
β-strand	108-112	5	7
β-strand	117	1	9
α-helix	118-119	2
β-strand	120-124	5	10
α-helix	125-127	3
α-helix	128-131	4
β-strand	135-145	11	10
β-strand	146	1	9
β-strand	151-156	6	11
β-strand	159-161	3	11
β-strand	165-169	5	10
α-helix	170-173	4
β-strand	179-188	10	10
α-helix	189-193	5
β-strand	197-203	7	11
β-strand	211-216	6	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mucin-1	A, a	protein	9	Homo sapiens	P15941 (AlphaFold model)
139H2 HC	H, h	protein	236	Homo sapiens
139H2 LC	L, l	protein	220	Homo sapiens

Sequence of entity 1 (A, a), FASTA

>8P6I_1 Mucin-1 (chains A, a)
APDTRPAPG

Sequence of entity 2 (H, h), FASTA

>8P6I_2 139H2 HC (chains H, h)
QVQLQQSGAELVKPGASVKLSCKASGYTFTNYYMYWVLQRPGQGLEWIGEINPSNGGTTF
NEKFKNKATLTVDKSSSTAYMQLNSLTSEDSAVYYCTRSRYGNYVNYGMDYWGQGTSVTV
SSASTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQ
SDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRDCGAAAHHHHHHHH

Sequence of entity 3 (L, l), FASTA

>8P6I_3 139H2 LC (chains L, l)
DIVMSQSPSSLAVSVGEKVTMSCKSSQSLLYSNTQKNYLAWYQQKPGQSPKLLIYWASTR
ESGVPDRFTGSGSGTDFTLTISSVKAENLAVYYCQQYYRYPPTFGGGTKLELKRADAAPT
VSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYS
MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Primary citation

Reverse-engineering the anti-MUC1 antibody 139H2 by mass spectrometry-based de novo sequencing. Peng, W., Giesbers, K.C., Siborova, M. et al. Life Sci Alliance (2024) 7. DOI 10.26508/lsa.202302366 · PubMed

Other PDB entries of the same protein (UniProt P15941 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6BSC 1.3 Å, Crystal structure of the Mucin-1 SEA domain
7V64 1.56 Å, Crystal structure of Antibody 16A in complex with MUC1 Glycopeptide(GlycoT)
6BSB 1.6 Å, Crystal structure of the Mucin-1 SEA domain, L1105M mutant, Selenium-derivative
6FZQ 1.7 Å, Crystal structure of scFv-SM3 in complex with compound 3
8S6K 1.75 Å, Crystal structure of ScFv-G2D11 complexed to a bis-Tn glycopeptide
6KX1 1.77 Å, Crystal structure of SN-101 mAb in complex with MUC1 glycopeptide
6FZR 1.8 Å, Crystal structure of scFv-SM3 in complex with compound 2
8AXH 1.85 Å, Crystal structure of a MUC1-like glycopeptide containing the unnatural…
8S6T 1.85 Å, Crystal structure of Fab-3F1 complexed to a bis-STn glycopeptide
1SM3 1.95 Å, Crystal structure of the tumor specific antibody SM3 complex with its peptide epitope
8S6V 1.95 Å, Crystal structure of Fab-2D9 chimera complexed to a bis-Tn glycopeptide
5T6P 1.97 Å, Crystal structure of therapeutic mAB AR20.5 in complex with MUC1 peptide

Browse structure collections

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