6LDY: Structure antibody D6

Structure antibody D6 in complex with methylated peptide. Determined by X-ray diffraction at 1.77 Å resolution. Released 25 Nov 2020.

Method: X-ray diffraction
Resolution: 1.77 Å
Organisms: Oryctolagus cuniculus, Homo sapiens
Chains: 6
Atoms: 7,265
Mol. weight: 105.63 kDa
Ligands: CA
Released: 25 Nov 2020

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

Secondary structure: helices and β-sheets

6LDY contains 42 α-helices and 93 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: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	1
β-strand	10-11	2	2
β-strand	17-24	8	1
β-strand	31	1	3
β-strand	32-38	7	4
β-strand	45-50	6	4
β-strand	56-58	3	4
β-strand	66-70	5	1
β-strand	74-79	6	1
α-helix	84-86	3
β-strand	88-95	8	4
β-strand	101-104	4	4
β-strand	108-110	3	4
β-strand	111-112	2	2
α-helix	116-117	2
β-strand	118	1	5
α-helix	119-120	2
β-strand	121-125	5	6
α-helix	132-133	2
β-strand	136-146	11	6
β-strand	147	1	5
β-strand	152-155	4	7
α-helix	156-158	3
β-strand	164-166	3	6
α-helix	167-169	3
β-strand	170-171	2	6
β-strand	177-186	10	6
α-helix	190-191	2
β-strand	192-198	7	7
α-helix	199-201	3
β-strand	203-209	7	7

Chain B: 12 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	8
α-helix	8	1
α-helix	10	1
β-strand	11-14	4	9
β-strand	19-25	7	8
α-helix	28-29	2
α-helix	30-32	3
β-strand	35-40	6	9
β-strand	47-51	5	9
β-strand	55-56	2	9
α-helix	57	1
β-strand	64-69	6	8
β-strand	72-77	6	8
α-helix	82-84	3
β-strand	86-95	10	9
β-strand	99-103	5	9
β-strand	107-112	6	9
β-strand	116	1	10
α-helix	117-118	2
β-strand	119-123	5	11
α-helix	124-126	3
α-helix	127-130	4
β-strand	134-144	11	11
β-strand	145	1	10
β-strand	149-154	6	12
β-strand	157-158	2	12
α-helix	159	1
β-strand	163-167	5	11
α-helix	168-171	4
β-strand	177-186	10	11
α-helix	187-190	4
β-strand	195-202	8	12
β-strand	205-212	8	12

Chains C and M: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	10	1	3
α-helix	11-13	3

Chain H: 8 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	13
β-strand	10-11	2	14
β-strand	17-24	8	13
β-strand	31	1	15
β-strand	32-38	7	16
β-strand	44-50	7	16
β-strand	56-58	3	16
α-helix	60-62	3
β-strand	66-70	5	13
β-strand	74-79	6	13
α-helix	84-86	3
β-strand	88-95	8	16
β-strand	101-104	4	16
β-strand	108-110	3	16
β-strand	111-112	2	14
α-helix	116-117	2
β-strand	118	1	17
β-strand	121-125	5	18
β-strand	129	1	19
β-strand	131	1	19
α-helix	132-133	2
β-strand	136-146	11	18
β-strand	147	1	17
β-strand	152-155	4	7
α-helix	156-158	3
β-strand	160	1	7
β-strand	164-166	3	18
α-helix	167-169	3
β-strand	170-171	2	18
β-strand	177-186	10	18
α-helix	189-191	3
β-strand	192-198	7	7
α-helix	199-201	3
β-strand	203-209	7	7

Chain L: 12 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	20
α-helix	8	1
α-helix	10	1
β-strand	11-14	4	21
β-strand	18-25	8	20
α-helix	28-29	2
α-helix	30-32	3
β-strand	35-40	6	21
β-strand	47-51	5	21
β-strand	55-56	2	21
α-helix	57	1
β-strand	64-69	6	20
β-strand	72-78	7	20
α-helix	82-84	3
β-strand	86-95	10	21
β-strand	99-103	5	21
β-strand	107-112	6	21
β-strand	116	1	22
α-helix	117-118	2
β-strand	119-123	5	23
α-helix	124-126	3
α-helix	127-130	4
β-strand	134-144	11	23
β-strand	145	1	22
β-strand	149-154	6	24
β-strand	157-158	2	24
α-helix	159	1
β-strand	163-167	5	23
α-helix	168-171	4
β-strand	177-186	10	23
α-helix	187-190	4
β-strand	195-202	8	24
β-strand	205-212	8	24

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab heavy chain	A, H	protein	241	Oryctolagus cuniculus
Fab light chain	B, L	protein	240	Oryctolagus cuniculus
Methylated peptide	C, M	protein	14	Homo sapiens	Q9Y2U5 (AlphaFold model)

Sequence of entity 1 (A, H), FASTA

>6LDY_1 Fab heavy chain (chains A, H)
QTVKESGGRLVTPGGTLTLTCTVSGFSLSRYAMSWVRQAPGEGLEYIGWINTYGSAYYAS
WVNGRFTISKTSTTMDLKMTSLTAADTATYFCVRWFADGGMDPWGPGTLVTVSSGQPKAP
SVFPLAPCCGDTPSSTVTLGCLVKGYLPEPVTVTWNSGTLTNGVRTFPSVRQSSGLYSLS
SVVSVTSSSQPVTCNVAHPATNTKVDKTVAPSTCSKPAAAEQKLISEEDLNSAVDHHHHH
H

Sequence of entity 2 (B, L), FASTA

>6LDY_2 Fab light chain (chains B, L)
ALVLTQTPSPVSAAVGGAVSISCQSSQNIYKDNELSWYQQKPGQPPKLLIYKASTLASGV
PSRFSGSGSGTQFTLTISGVQCDDAATYYCQGSRYNNGWDSGFGGGTEVVVKGDPVAPTV
LIFPPSADLVATGTVTIVCVANKYFPDVTVTWEVDGTTQTTGIENSKTPQNSADCTYNLS
STLTLTSTQYNSHKEYTCKVTQGTTSVVQSFNRGDCAAAEQKLISEEDLNSAVDHHHHHH

Sequence of entity 3 (C, M), FASTA

>6LDY_3 Methylated peptide (chains C, M)
NPIFEKFGKGGTYP

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	2

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

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:

6LDW 1.6 Å, Structure of antibody C9 in complex with methylated peptide
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…
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

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