1R3J: Antibody Fab fragment light chain

potassium channel KcsA-Fab complex in high concentration of Tl+. Determined by X-ray diffraction at 1.9 Å resolution. Released 25 Nov 2003.

Method: X-ray diffraction
Resolution: 1.9 Å
Organisms: Mus musculus, Streptomyces lividans
Chains: 3
Atoms: 4,400
Mol. weight: 61.85 kDa
Ligands: F09, TL, DGA
Released: 25 Nov 2003

Explore 1R3J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1R3J contains 17 α-helices and 43 β-strands across 3 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, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	1
β-strand	10-13	4	2
β-strand	19-25	7	1
β-strand	33-38	6	2
β-strand	45-49	5	2
β-strand	53-54	2	2
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	111	1	3
β-strand	114-118	5	4
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	4
β-strand	140	1	3
β-strand	145-150	6	5
β-strand	153-155	3	5
β-strand	159-163	5	4
α-helix	164-167	4
β-strand	173-182	10	4
α-helix	183-187	5
β-strand	191-197	7	5
α-helix	204	1
β-strand	205-210	6	5

Chain B: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	6
β-strand	9-12	4	7
β-strand	18-24	7	6
β-strand	33-39	7	7
β-strand	46-52	7	7
β-strand	57-60	4	7
β-strand	68-73	6	6
β-strand	78-83	6	6
α-helix	88-90	3
β-strand	92-99	8	7
β-strand	107-108	2	7
β-strand	112-116	5	7
α-helix	120-121	2
β-strand	122	1	8
α-helix	123-124	2
β-strand	125-129	5	9
β-strand	140-150	11	9
β-strand	151	1	8
β-strand	156-159	4	10
α-helix	160-162	3
β-strand	164	1	10
β-strand	168-170	3	9
α-helix	171-173	3
β-strand	174-175	2	9
β-strand	180-189	10	9
α-helix	190-192	3
β-strand	199-204	6	10
α-helix	205-207	3
β-strand	209-214	6	10

Chain C: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	24-51	28
α-helix	62-73	12
α-helix	86-121	36

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Antibody Fab fragment light chain	A	protein	212	Mus musculus	P01837 (AlphaFold model)
Antibody Fab fragment heavy chain	B	protein	219	Mus musculus	P01868 (AlphaFold model)
Voltage-gated potassium channel	C	protein	124	Streptomyces lividans	P0A334 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1R3J_1 Antibody Fab fragment light chain (chains A)
DILLTQSPAILSVSPGERVSFSCRASQSIGTDIHWYQQRTNGSPRLLIKYASESISGIPS
RFSGSGSGTDFTLSINSVESEDIANYYCQQSNRWPFTFGSGTKLEIKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRN

Sequence of entity 2 (B), FASTA

>1R3J_2 Antibody Fab fragment heavy chain (chains B)
QVQLQQPGAELVKPGASVKLSCKASGYTFTSDWIHWVKQRPGHGLEWIGEIIPSYGRANY
NEKIQKKATLTADKSSSTAFMQLSSLTSEDSAVYYCARERGDGYFAVWGAGTTVTVSSAK
TTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLY
TLSSSVTVPSSSWPSETVTCNVAHPASSTKVDKKIVPRD

Sequence of entity 3 (C), FASTA

>1R3J_3 Voltage-gated potassium channel (chains C)
MAPMLSGLLARLVKLLLGRHGSALHWRAAGAATVLLVIVLLAGSYLAVLAERGAPGAQLI
TYPRALWWSVETATTVGYGDLYPVTLWGRCVAVVVMVAGITSFGLVTAALATWFVGREQE
RRGH

Ligands and cofactors

ID	Name	Formula	Copies
F09	Nonan-1-ol	C9 H20 O	1
TL	Thallium (I) ion	Tl	5
DGA	Diacyl glycerol	C39 H76 O5	1

Primary citation

The occupancy of ions in the K+ selectivity filter: Charge balance and coupling of ion binding to a protein conformational change underlie high conduction rates. Zhou, Y., MacKinnon, R. J Mol Biol (2003) 333:965-975. DOI 10.1016/j.jmb.2003.09.022 · 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
1RUR 1.5 Å, Crystal Structure (I) of native Diels-Alder antibody 13G5 Fab at pH 8.0 with a data set…
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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