1XGY: Anti-Meta I Rhodopsin Fab Fragment K42-41L

Crystal Structure of Anti-Meta I Rhodopsin Fab Fragment K42-41L. Determined by X-ray diffraction at 2.71 Å resolution. Released 27 Sept 2005.

Method: X-ray diffraction
Resolution: 2.71 Å
Organism: Mus musculus
Chains: 6
Atoms: 6,778
Mol. weight: 96.89 kDa
Released: 27 Sept 2005

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

Secondary structure: helices and β-sheets

1XGY contains 36 α-helices and 92 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 H: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	8
β-strand	10-12	3	2
β-strand	18-25	8	8
α-helix	29-31	3
β-strand	34-39	6	2
β-strand	45-52	8	2
β-strand	56-59	4	2
α-helix	61-63	3
β-strand	67-72	6	8
α-helix	73-75	3
β-strand	77-82	6	8
α-helix	84-86	3
β-strand	88-94	7	2
β-strand	102-103	2	2
β-strand	107-111	5	2
α-helix	114-116	3
β-strand	117	1	9
β-strand	120-124	5	10
β-strand	135-145	11	10
β-strand	146	1	9
β-strand	151-154	4	11
α-helix	155-157	3
β-strand	163-165	3	10
α-helix	166-168	3
β-strand	169-171	3	10
β-strand	174-184	11	10
α-helix	185-187	3
β-strand	194-199	6	11
α-helix	200-202	3
β-strand	204-209	6	11

Chain I: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	19
β-strand	10-12	3	20
β-strand	18-25	8	19
α-helix	29-31	3
β-strand	34-40	7	20
β-strand	43-52	10	20
β-strand	56-59	4	20
α-helix	61-63	3
β-strand	67-72	6	19
β-strand	77-82	6	19
β-strand	88-94	7	20
β-strand	102-103	2	20
β-strand	107-111	5	20
β-strand	117	1	21
β-strand	120-124	5	22
β-strand	135-145	11	22
β-strand	146	1	21
β-strand	151-154	4	23
α-helix	155-157	3
β-strand	164-165	2	22
α-helix	166-168	3
β-strand	169-171	3	22
β-strand	174-184	11	22
α-helix	185-187	3
β-strand	194-199	6	23
α-helix	200-202	3
β-strand	204-209	6	23
α-helix	211-213	3

Chain L: 8 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	1
β-strand	9	1	2
β-strand	13	1	3
β-strand	19-25	7	1
β-strand	27C	1	4
β-strand	31	1	4
β-strand	33-38	6	2
β-strand	45-49	5	2
β-strand	53-54	2	2
α-helix	55	1
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	102-103	2	2
β-strand	106	1	3
β-strand	111	1	5
β-strand	114-118	5	6
α-helix	119-121	3
α-helix	124-126	3
β-strand	129-139	11	6
β-strand	140	1	5
β-strand	144-150	7	7
β-strand	154-155	2	7
β-strand	159-163	5	6
α-helix	164-167	4
β-strand	173-182	10	6
α-helix	183-187	5
β-strand	191-198	8	7
α-helix	204	1
β-strand	205-210	6	7

Chain M: 10 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	12
β-strand	9	1	13
α-helix	10-12	3
β-strand	13	1	14
β-strand	19-25	7	12
β-strand	27C	1	15
β-strand	31	1	15
β-strand	33-38	6	13
β-strand	45-49	5	13
β-strand	53-54	2	13
β-strand	62-67	6	12
β-strand	70-75	6	12
α-helix	80-82	3
β-strand	85-90	6	13
α-helix	96	1
β-strand	97-98	2	13
β-strand	103	1	13
α-helix	105	1
β-strand	106	1	14
α-helix	107	1
β-strand	111	1	16
β-strand	114-118	5	17
α-helix	119-121	3
α-helix	124-126	3
β-strand	129-139	11	17
β-strand	140	1	16
β-strand	144-150	7	18
β-strand	153-155	3	18
β-strand	159-163	5	17
α-helix	164-167	4
β-strand	173-182	10	17
α-helix	183-188	6
β-strand	191-198	8	18
α-helix	204	1
β-strand	205-210	6	18

Chains P and Q: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
K42-41L Fab Light Chain	L, M	protein	216	Mus musculus
K42-41L Fab Heavy Chain	H, I	protein	219	Mus musculus	Q6PF95 (AlphaFold model)
Rhodopsin Epitope Mimetic Peptide	P, Q	protein	9

Sequence of entity 1 (L, M), FASTA

>1XGY_1 K42-41L Fab Light Chain (chains L, M)
DIVMTQAAFSNPVTLGTSASISCRSSKSLLHSNGITYLYWYLQRPGQSPQLLIYRMSNLA
SGVPDRFSGSGSGTDFALRISRVEAEDVGVYYCGQMLEHPLTFGTGTKLELKRADAAPTV
SIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSM
SSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR

Sequence of entity 2 (H, I), FASTA

>1XGY_2 K42-41L Fab Heavy Chain (chains H, I)
QVQLQQSGPELVRPGASVKISCKASGYTFTDYYINWVKQRPGQGLEWIGWIFPRNGNTKY
NEKFKGKATLTVDKSSSTAFMQLSSLTSEDSAVYFCATTVSYVMDYWGQGTTVTVSSAKT
TPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYT
LSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDC

Sequence of entity 3 (P, Q), FASTA

>1XGY_3 Rhodopsin Epitope Mimetic Peptide (chains P, Q)
TGALQERSK

Primary citation

Equilibrium between metarhodopsin-I and metarhodopsin-II is dependent on the conformation of the third cytoplasmic loop. Piscitelli, C.L., Angel, T.E., Bailey, B.W. et al. J Biol Chem (2006) 281:6813-6825. DOI 10.1074/jbc.M510175200 · PubMed

Other PDB entries of the same protein (UniProt Q6PF95 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1EJO 2.3 Å, FAB fragment of neutralising monoclonal antibody 4C4 complexed with G-H loop from fmdv.
1JN6 2.7 Å, Crystal Structure of Fab-Estradiol Complexes
2GSI 2.81 Å, Crystal Structure of a Murine Fab in Complex with an 11 Residue Peptide Derived from…
2A6K 3.0 Å, Crystal Structure Analysis of the germline antibody 36-65 Fab in complex with the…

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