2A6K: Germline antibody 36-65 Fab light chain

Crystal Structure Analysis of the germline antibody 36-65 Fab in complex with the dodecapeptide SLGDNLTNHNLR. Determined by X-ray diffraction at 3.0 Å resolution. Released 13 Jun 2006.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Mus musculus
Chains: 5
Atoms: 6,764
Mol. weight: 96.66 kDa
Released: 13 Jun 2006

Explore 2A6K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2A6K contains 25 α-helices and 85 β-strands across 4 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: 6 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-5	2	1
β-strand	10-13	4	2
β-strand	20-25	6	1
β-strand	33-38	6	2
β-strand	44-48	5	2
β-strand	49	1	3
β-strand	54	1	3
β-strand	62-67	6	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	85-90	6	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	122-126	5
β-strand	129-139	11	4
β-strand	145-150	6	5
β-strand	153	1	5
β-strand	159-163	5	4
α-helix	165-167	3
β-strand	173-182	10	4
α-helix	183-187	5
β-strand	191-198	8	5
β-strand	201-210	10	5

Chain B: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	6
α-helix	7-9	3
β-strand	10-11	2	7
β-strand	17-25	9	6
α-helix	29-31	3
β-strand	34-39	6	7
β-strand	45-52	8	7
β-strand	57-60	4	7
β-strand	65	1	6
β-strand	68-73	6	6
β-strand	78-84	7	6
α-helix	88-90	3
β-strand	92-100	9	7
β-strand	107-111	5	7
β-strand	115-118	4	7
β-strand	125	1	8
β-strand	128-132	5	9
β-strand	143-153	11	9
β-strand	154	1	8
β-strand	159-162	4	10
α-helix	163-165	3
β-strand	171-173	3	9
α-helix	174-176	3
β-strand	177-178	2	9
β-strand	183-192	10	9
β-strand	202-207	6	10
α-helix	208-210	3
β-strand	212-217	6	10

Chain H: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	16
α-helix	6-9	4
β-strand	10-11	2	17
β-strand	18-20	3	16
β-strand	23-25	3	16
α-helix	29-31	3
β-strand	34-39	6	17
β-strand	45-51	7	17
β-strand	58-60	3	17
β-strand	65	1	16
β-strand	68-73	6	16
β-strand	78-83	6	16
α-helix	88-90	3
β-strand	92-103	12	17
β-strand	105-111	7	17
β-strand	115-118	4	17
β-strand	125	1	18
β-strand	128-132	5	19
β-strand	143-153	11	19
β-strand	154	1	18
β-strand	159-162	4	20
α-helix	163-165	3
β-strand	172-173	2	19
α-helix	174-176	3
β-strand	177-178	2	19
β-strand	183-192	10	19
β-strand	202-207	6	20
α-helix	208-210	3
β-strand	212-217	6	20

Chain L: 7 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	11
β-strand	10-13	4	12
β-strand	20-24	5	11
β-strand	33-38	6	12
β-strand	44-48	5	12
β-strand	49	1	13
β-strand	54	1	13
β-strand	62-67	6	11
β-strand	70-75	6	11
α-helix	80-82	3
β-strand	85-90	6	12
α-helix	96	1
β-strand	97-98	2	12
β-strand	102-106	5	12
β-strand	114-118	5	14
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	14
β-strand	145-150	6	15
β-strand	154-155	2	15
β-strand	159-163	5	14
α-helix	164-167	4
β-strand	173-182	10	14
α-helix	183-186	4
β-strand	191-197	7	15
α-helix	204	1
β-strand	205-210	6	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Germline antibody 36-65 Fab light chain	A, L	protein	214	Mus musculus	P01837 (AlphaFold model)
Germline antibody 36-65 Fab heavy chain	B, H	protein	222	Mus musculus	Q6PF95 (AlphaFold model)
Dodecapeptide: slgdnltnhnlr	P	protein	12

Sequence of entity 1 (A, L), FASTA

>2A6K_1 Germline antibody 36-65 Fab light chain (chains A, L)
DIQMTQTTSSLSASLGDRVTISCRASQDISNYLNWYQQKPDGTVKLLIYYTSRLHSGVPS
RFSGSGSGTDYSLTISNLEQEDIATYFCQQGNTLPRTFGGGTKLEIKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 2 (B, H), FASTA

>2A6K_2 Germline antibody 36-65 Fab heavy chain (chains B, H)
EVQLQQSGAELVRAGSSVKMSCKASGYTFTSYGINWVKQRPGQGLEWIGYINPGNGYTKY
NEKFKGKTTLTVDKSSSTAYMQLRSLTSEDSAVYFCARSVYYGGSYYFDYWGQGTTLTVS
SAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQS
DLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRD

Sequence of entity 3 (P), FASTA

>2A6K_3 DODECAPEPTIDE: SLGDNLTNHNLR (chains P)
SLGDNLTNHNLR

Primary citation

Differential epitope positioning within the germline antibody paratope enhances promiscuity in the primary immune response. Sethi, D.K., Agarwal, A., Manivel, V. et al. Immunity (2006) 24:429-438. DOI 10.1016/j.immuni.2006.02.010 · PubMed

Other PDB entries of the same protein (UniProt P01837 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3D9A 1.2 Å, High Resolution Crystal Structure Structure of HyHel10 Fab Complexed to Hen Egg Lysozyme
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2AJU 1.5 Å, Cyrstal structure of cocaine catalytic antibody 7A1 Fab'
2AJV 1.5 Å, Crystal Structure of Cocaine catalytic Antibody 7A1 Fab' in Complex with Cocaine
2W60 1.5 Å, Anti citrullinated Collagen type 2 antibody acc4
2W9D 1.57 Å, Structure of Fab fragment of the ICSM 18 - anti-Prp therapeutic antibody at 1.57 A…
3BKJ 1.59 Å, Crystal structure of Fab wo2 bound to the n terminal domain of amyloid beta peptide (1-16)
3BAE 1.59 Å, Crystal structure of Fab WO2 bound to the N terminal domain of Amyloid beta peptide (1-28)
2R1Y 1.6 Å, Crystal structure of S25-2 Fab in complex with Kdo analogues
2R2B 1.6 Å, Crystal structure of S25-2 Fab in complex with Kdo analogues
3BKM 1.6 Å, Structure of anti-amyloid-beta Fab WO2 (Form A, P212121)
3CFB 1.6 Å, High-resolution structure of blue fluorescent antibody EP2-19G2 in complex with stilbene…

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