6LDW: Antibody C9

Structure of antibody C9 in complex with methylated peptide. Determined by X-ray diffraction at 1.6 Å resolution. Released 25 Nov 2020.

Method: X-ray diffraction
Resolution: 1.6 Å
Organisms: Oryctolagus cuniculus, Homo sapiens
Chains: 6
Atoms: 6,937
Mol. weight: 104.29 kDa
Released: 25 Nov 2020

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

Secondary structure: helices and β-sheets

6LDW contains 37 α-helices and 94 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: 12 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	13
β-strand	10-14	5	14
β-strand	19-25	7	13
α-helix	28-29	2
α-helix	30-32	3
β-strand	35-40	6	14
β-strand	47-51	5	14
β-strand	55-56	2	14
α-helix	57	1
β-strand	64-69	6	13
β-strand	72-77	6	13
α-helix	82-84	3
β-strand	86-92	7	14
β-strand	94	1	15
β-strand	98	1	15
α-helix	100	1
β-strand	101	1	14
α-helix	102	1
β-strand	105-110	6	14
β-strand	114	1	16
α-helix	115-116	2
β-strand	117-121	5	17
α-helix	122-124	3
α-helix	127-129	3
β-strand	132-142	11	17
β-strand	143	1	16
β-strand	147-152	6	18
β-strand	155-156	2	18
α-helix	157	1
β-strand	161-165	5	17
α-helix	166-169	4
β-strand	175-184	10	17
α-helix	185-188	4
β-strand	193-200	8	18
β-strand	203-210	8	18

Chain B: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	19
β-strand	10-11	2	20
β-strand	17-24	8	19
β-strand	33-38	6	21
β-strand	45-50	6	21
β-strand	57-59	3	21
α-helix	61-63	3
β-strand	64	1	19
β-strand	67-71	5	19
β-strand	76-80	5	19
α-helix	85-87	3
β-strand	89-95	7	21
β-strand	101-102	2	21
β-strand	106-108	3	21
β-strand	109-110	2	20
β-strand	116	1	22
α-helix	117-118	2
β-strand	119-123	5	23
β-strand	136-144	9	23
β-strand	145	1	22
β-strand	150-153	4	24
α-helix	154-156	3
β-strand	158	1	24
β-strand	162-164	3	23
α-helix	165-167	3
β-strand	168-169	2	23
β-strand	175-182	8	23
β-strand	190-196	7	24
α-helix	197-199	3
β-strand	201-207	7	24

Chains C and D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2

Chain H: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	7
β-strand	10-11	2	8
β-strand	17-24	8	7
β-strand	33-38	6	9
β-strand	44-50	7	9
β-strand	57-59	3	9
α-helix	61-63	3
β-strand	64	1	7
β-strand	67-71	5	7
β-strand	76-80	5	7
α-helix	85-87	3
β-strand	89-95	7	9
β-strand	101-102	2	9
β-strand	106-108	3	9
β-strand	109-110	2	8
β-strand	116	1	10
α-helix	117-118	2
β-strand	119-123	5	11
β-strand	136-144	9	11
β-strand	145	1	10
β-strand	150-153	4	12
α-helix	154-156	3
β-strand	158	1	12
β-strand	162-164	3	11
α-helix	165-167	3
β-strand	168-169	2	11
β-strand	175-182	8	11
β-strand	190-196	7	12
α-helix	197-199	3
β-strand	201-207	7	12

Chain L: 11 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-14	5	2
β-strand	19-25	7	1
α-helix	28-29	2
α-helix	30-32	3
β-strand	35-40	6	2
β-strand	47-51	5	2
β-strand	55-56	2	2
α-helix	57	1
β-strand	64-69	6	1
β-strand	72-77	6	1
α-helix	82-84	3
β-strand	86-92	7	2
β-strand	94	1	3
β-strand	98	1	3
α-helix	100	1
β-strand	101	1	2
α-helix	102	1
β-strand	105-110	6	2
β-strand	114	1	4
α-helix	115-116	2
β-strand	117-121	5	5
α-helix	122-124	3
α-helix	125-128	4
β-strand	132-142	11	5
β-strand	143	1	4
β-strand	147-152	6	6
β-strand	155-156	2	6
β-strand	161-165	5	5
α-helix	166-169	4
β-strand	175-184	10	5
α-helix	185-190	6
β-strand	193-200	8	6
β-strand	203-210	8	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab light chain	A, L	protein	238	Oryctolagus cuniculus
Fab heavy chain	B, H	protein	239	Oryctolagus cuniculus
Ile-phe-glu-lys-phe-gly-M3L-gly-gly	C, D	protein	14	Homo sapiens	Q9Y2U5 (AlphaFold model)

Sequence of entity 1 (A, L), FASTA

>6LDW_1 Fab light chain (chains A, L)
AQVLTQTPSSVSAAVGGTVTINCQASQSVYNNNWLGWYQQKPGQPPKLLIYKASTLASGV
PSRFRGSGSGTQFTLTISDVQCDDAATYYCAGGYNGNIFPFGGGTEVVVTGDPVAPTVLI
FPPAADQVATGTVTIVCVANKYFPDVTVTWEVDGTTQTTGIENSKTPQNSADCTYNLSST
LTLTSTQYNSHKEYTCKVTLGTTSVVQSFNRGDCAAAEQKLISEEDLNSAVDHHHHHH

Sequence of entity 2 (B, H), FASTA

>6LDW_2 Fab heavy chain (chains B, H)
QSVEESGGRLVTPGTPLTLTCTVSGFSLTSYDMSWVRQAPGKGLEYIGFISSTTGGTYYA
SWAKGRFTISKTSTTVDLKITSPTTEDTATYFCAAGSWYNMWGPGTLVTVSSGQPKAPSV
FPLAPCCGDTPSSTMTLGCLVKGYLPEPVTVTWNSGTLTNGVRTFPSVRQSSGLYSLSSV
VSVTSSSQPVTCNVAHPATNTKVDKTVAPSTCSKPAAAEQKLISEEDLNSAVDHHHHHH

Sequence of entity 3 (C, D), FASTA

>6LDW_3 ILE-PHE-GLU-LYS-PHE-GLY-M3L-GLY-GLY (chains C, D)
NPIFEKFGKGGTYP

Primary citation

Structural basis for antigen recognition by methylated lysine-specific antibodies. Ishii, M., Nakakido, M., Caaveiro, J.M.M. et al. J Biol Chem (2020) 296:100176-100176. DOI 10.1074/jbc.RA120.015996 · PubMed

Other PDB entries of the same protein (UniProt Q9Y2U5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5HQ8 1.72 Å, Co-crystal Structure of human SMYD3 with a MEKK2 peptide at 2.13A
2NPT 1.75 Å, Crystal Structure of the complex of human mitogen activated protein kinase kinase 5 phox…
6LDY 1.77 Å, Structure antibody D6 in complex with methylated peptide
6LDX 1.8 Å, Structure antibody E6 in complex with methylated peptide
6LDV 1.9 Å, Structure antibody F9 in complex with methylated peptide
9P6A 2.4 Å, The catalytic domain of MEKK2 in complex with ponatinib
5EX0 2.7 Å, Crystal structure of human SMYD3 in complex with a MAP3K2 peptide
2CU1 Solution structure of the PB1 domain of human protein kinase MEKK2b

Browse structure collections

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