6LDV: Structure antibody F9

Structure antibody F9 in complex with methylated peptide. Determined by X-ray diffraction at 1.9 Å resolution. Released 25 Nov 2020.

Method: X-ray diffraction
Resolution: 1.9 Å
Organisms: Oryctolagus cuniculus, Homo sapiens
Chains: 3
Atoms: 3,549
Mol. weight: 53.45 kDa
Released: 25 Nov 2020

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

Secondary structure: helices and β-sheets

6LDV contains 16 α-helices and 44 β-strands across 2 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: 6 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	33-38	6	3
β-strand	45-50	6	3
β-strand	56-58	3	3
α-helix	60-62	3
β-strand	66-70	5	1
β-strand	74-79	6	1
α-helix	84-86	3
β-strand	88-95	8	3
α-helix	96	1
β-strand	101-104	4	3
β-strand	108-110	3	3
β-strand	111-112	2	2
β-strand	118	1	4
β-strand	121-125	5	5
β-strand	137-146	10	5
β-strand	147	1	4
β-strand	152-155	4	6
α-helix	156-158	3
β-strand	160	1	6
β-strand	165-166	2	5
α-helix	167-169	3
β-strand	170-171	2	5
β-strand	177-185	9	5
β-strand	192-198	7	6
α-helix	199-201	3
β-strand	203-209	7	6

Chain L: 10 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	7
α-helix	8	1
α-helix	10	1
β-strand	11-14	4	8
β-strand	19-25	7	7
α-helix	28-29	2
α-helix	30-32	3
β-strand	35-40	6	8
β-strand	47-51	5	8
β-strand	55-56	2	8
α-helix	57	1
β-strand	64-69	6	7
β-strand	72-77	6	7
α-helix	82-84	3
β-strand	86-93	8	8
β-strand	100-102	3	8
β-strand	106-111	6	8
β-strand	115	1	9
β-strand	118-122	5	10
α-helix	123-125	3
α-helix	126-130	5
β-strand	133-143	11	10
β-strand	144	1	9
β-strand	148-153	6	11
β-strand	156-158	3	11
β-strand	162-166	5	10
α-helix	167-170	4
β-strand	176-185	10	10
α-helix	186-190	5
β-strand	194-201	8	11
β-strand	204-211	8	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab heavy chain	H	protein	241	Oryctolagus cuniculus
Fab light chain	L	protein	239	Oryctolagus cuniculus
Gly-M3L-gly-gly-thr-tyr-pro	P	protein	14	Homo sapiens	Q9Y2U5 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>6LDV_1 Fab heavy chain (chains H)
QSVEESGGRLVTPGTPLTLTCTVSGFSLNSNAISWVRQAPGEGLEWVGAIYTHGSTVYAN
WAKGRFTISKTSTTIELKMTSLTTEDTATYFCARHGYTYSFNLWGPGTLVTVSSGQPKAP
SVFPLAPCCGDTPSSTVTLGCLVKGYLPEPVTVTWNSGTLTNGVRTFPSVRQSSGLYSLS
SVVSVTSSSQPVTCNVAHPATNTKVDKTVAPSTCSKPAAAEQKLISEEDLNSAVDHHHHH
H

Sequence of entity 2 (L), FASTA

>6LDV_2 Fab light chain (chains L)
AQGLTQTPSPVSAALGGTVTINCQSSQSVYGNNRLAWYQQKPGQPPKRLIYQASTLDSGV
PSRFSGSGSGTQFTLTISGVQCDDAATYYCQGGYSSGDAWAFGGGTEVVVKGDPVAPTVL
IFPPSADLVATGTVTIVCVANKYFPDVTVTWEVDGTTQTTGIENSKTPQNSADCTYNLSS
TLTLTSTQYNSHKEYTCKVTQGTTSVVQSFNRGDCAAAEQKLISEEDLNSAVDHHHHHH

Sequence of entity 3 (P), FASTA

>6LDV_3 GLY-M3L-GLY-GLY-THR-TYR-PRO (chains P)
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:

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…
6LDY 1.77 Å, Structure antibody D6 in complex with methylated peptide
6LDX 1.8 Å, Structure antibody E6 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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