1YMH: Anti-HCV Fab 19D9D6

anti-HCV Fab 19D9D6 complexed with protein L (PpL) mutant A66W. Determined by X-ray diffraction at 2.6 Å resolution. Released 31 May 2005.

Method: X-ray diffraction
Resolution: 2.6 Å
Organisms: Mus musculus, Finegoldia magna
Chains: 6
Atoms: 7,884
Mol. weight: 110.42 kDa
Released: 31 May 2005

Explore 1YMH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1YMH contains 29 α-helices and 106 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: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-13	4	2
α-helix	17-18	2
β-strand	19-25	7	1
β-strand	27C-27D	2	3
β-strand	30-31	2	3
β-strand	33-38	6	2
β-strand	45-49	5	2
β-strand	53-54	2	2
α-helix	55	1
β-strand	62-67	6	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	84-90	7	2
α-helix	96	1
β-strand	97-98	2	2
β-strand	102-106	5	2
β-strand	114-118	5	4
α-helix	122-125	4
β-strand	132-139	8	4
β-strand	145	1	5
β-strand	148-149	2	6
β-strand	155	1	6
β-strand	159-163	5	4
β-strand	173-179	7	4
α-helix	183-186	4
β-strand	193-196	4	6
β-strand	197	1	5
α-helix	204	1
β-strand	205-208	4	6

Chain B: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	7
α-helix	7-9	3
β-strand	10-12	3	8
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	34-39	6	8
β-strand	46-51	6	8
β-strand	57-59	3	8
α-helix	61-63	3
β-strand	67-72	6	7
α-helix	73-75	3
β-strand	77-82	6	7
α-helix	84-86	3
β-strand	88-95	8	8
β-strand	100A-103	4	8
β-strand	107-111	5	8
α-helix	114-116	3
β-strand	117	1	9
β-strand	121-124	4	10
β-strand	135-145	11	10
β-strand	146	1	9
β-strand	151-154	4	11
α-helix	155-157	3
β-strand	159	1	11
β-strand	163-165	3	10
β-strand	170	1	10
β-strand	175-184	10	10
α-helix	185-187	3
β-strand	194-199	6	11
α-helix	200-202	3
β-strand	204-209	6	11

Chain C: 6 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	12
β-strand	10-14	5	13
β-strand	19-25	7	12
β-strand	27C-27D	2	14
β-strand	30-31	2	14
β-strand	33-38	6	13
β-strand	45-49	5	13
β-strand	53-54	2	13
α-helix	55	1
β-strand	62-67	6	12
β-strand	70-75	6	12
α-helix	80-82	3
β-strand	84-90	7	13
α-helix	96	1
β-strand	97-98	2	13
β-strand	102-107	6	13
β-strand	111	1	15
β-strand	114-118	5	16
α-helix	122-126	5
β-strand	129-137	9	16
β-strand	139	1	17
β-strand	140	1	15
β-strand	145-147	3	18
β-strand	159-160	2	16
β-strand	163	1	19
β-strand	173	1	17
β-strand	175	1	19
β-strand	176-182	7	16
α-helix	183-187	5
β-strand	191-197	7	18
β-strand	206-210	5	18
α-helix	211-213	3

Chain D: 5 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	20
β-strand	10-12	3	21
β-strand	18-25	8	20
α-helix	29-31	3
β-strand	34-39	6	21
β-strand	46-51	6	21
β-strand	57-59	3	21
β-strand	67-72	6	20
α-helix	73-75	3
β-strand	77-82	6	20
α-helix	84-86	3
β-strand	88-95	8	21
β-strand	100A-103	4	21
β-strand	107-111	5	21
β-strand	117	1	22
β-strand	120-124	5	23
β-strand	136-145	10	23
β-strand	146	1	22
β-strand	151-154	4	24
β-strand	163-165	3	23
α-helix	166-168	3
β-strand	169-171	3	23
β-strand	174-183	10	23
β-strand	194-199	6	24
α-helix	200-202	3
β-strand	204-209	6	24

Chain E: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	822-828	7	2
β-strand	834-840	7	2
α-helix	843-861	19
β-strand	864-869	6	2
β-strand	874-879	6	2

Chain F: 1 helix, 10 β-strands

Element	Residues	Length	Sheet
β-strand	822-823	2	25
β-strand	824-825	2	26
β-strand	826-828	3	27
β-strand	834-836	3	27
β-strand	838	1	13
β-strand	839-840	2	25
α-helix	843-858	16
β-strand	864-865	2	27
β-strand	868	1	26
β-strand	874-875	2	26
β-strand	878-879	2	27

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab 16D9D6, light chain	A, C	protein	220	Mus musculus
Fab 16D9D6, heavy chain	B, D	protein	218	Mus musculus
Protein L	E, F	protein	65	Finegoldia magna	Q51918 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>1YMH_1 Fab 16D9D6, light chain (chains A, C)
DIVMSQSPSSLAVSAGEKVTMSCKSSQSLLNSRTRKNYLAWYQQKPGQSPKVLIYWASTR
ESGVPDRFTGRGSGTDFTLTISSVQAEDQAVYYCKQAYIPPLTFGAGTKLELKRADAAPT
VSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYS
MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 2 (B, D), FASTA

>1YMH_2 Fab 16D9D6, heavy chain (chains B, D)
QIQLVQSGPELKKPGETVKISCKASGYTFTDFSMHWVNQAPGKGLNWMGWVNTETGEPTY
ADDFKGRFAFSLETSASTAYLQINSLKNEDTATYFCARFLLRQYFDVWGAGTTVTVSSAK
TTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLY
TLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR

Sequence of entity 3 (E, F), FASTA

>1YMH_3 Protein L (chains E, F)
KEEVTIKVNLIFADGKIQTAEFKGTFEEATAEAYRYADLLAKVNGEYTWDLEDGGNHMNI
KFAGK

Primary citation

Comparison of the crystallization and crystal packing of two Fab single-site mutant protein L complexes. Granata, V., Housden, N.G., Harrison, S. et al. Acta Crystallogr D Biol Crystallogr (2005) 61:750-754. DOI 10.1107/S0907444905007110 · PubMed

Other PDB entries of the same protein (UniProt Q51918 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5U6A 1.74 Å, Crystal structure of I83E meditope-enabled trastuzumab with azido-PEG3-meditope
5U3D 1.77 Å, Structure of meditope enabled trastuzumab I83E variant
5U5F 1.81 Å, Meditope enabled trastuzumab I83E variant in complex with (ac) CQFDA(PH)2STRRLRCGGSK
6B9Z 1.82 Å, Trastuzumab Fab v3
5U5M 1.88 Å, Crystal structure of I83E meditope-enabled trastuzumab with azido-meditope
6BAH 1.9 Å, Trastuzumab Fab v3 with 5-diphenyl meditope variant
4IOI 1.95 Å, Meditope-enabled trastuzumab in complex with CQFDLSTRRLKC
4HJG 2.0 Å, Meditope-enabled trastuzumab
4HKZ 2.08 Å, Trastuzumab Fab complexed with Protein L and Protein A fragments
6B9Y 2.14 Å, Trastuzumab Fab v3 in complex with 5-phenyl meditope variant
6BAE 2.14 Å, Trastuzumab Fab v3 in complex with CQFDLSTRRLKC
1HEZ 2.7 Å, Structure of P. magnus protein L bound to a human IgM Fab.

Browse structure collections

About this viewer

MolViewer shows 1YMH directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.