6PLH: FAB fragment

FAB fragment complexed with C-mannosylated tryptophan peptide. Determined by X-ray diffraction at 1.6 Å resolution. Released 8 Jul 2020.

Method: X-ray diffraction
Resolution: 1.6 Å
Organisms: Mus musculus, Homo sapiens
Chains: 3
Atoms: 3,855
Mol. weight: 52.6 kDa
Ligands: MAN, PO4
Released: 8 Jul 2020

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

Secondary structure: helices and β-sheets

6PLH contains 19 α-helices and 47 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: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-13	4	2
β-strand	19-25	7	1
β-strand	30	1	3
β-strand	36	1	3
β-strand	38-43	6	2
β-strand	50-54	5	2
β-strand	58-59	2	2
α-helix	60	1
β-strand	67-72	6	1
β-strand	75-80	6	1
α-helix	85-87	3
β-strand	89-95	7	2
β-strand	98	1	4
α-helix	101	1
β-strand	102-103	2	2
β-strand	107-111	5	2
β-strand	116	1	5
α-helix	117-118	2
β-strand	119-123	5	6
α-helix	124-126	3
α-helix	127-130	4
β-strand	134-144	11	6
β-strand	145	1	5
β-strand	149-155	7	7
β-strand	158-160	3	7
β-strand	164-168	5	6
α-helix	169-172	4
β-strand	178-187	10	6
α-helix	188-191	4
β-strand	196-203	8	7
α-helix	209	1
β-strand	210-215	6	7

Chain B: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	8
β-strand	9-12	4	9
β-strand	18-25	8	8
α-helix	29-31	3
β-strand	34-39	6	9
β-strand	46-51	6	9
β-strand	58-60	3	9
α-helix	62-64	3
β-strand	68-73	6	8
β-strand	78-83	6	8
α-helix	88-90	3
β-strand	92-99	8	9
α-helix	100	1
β-strand	105-108	4	9
β-strand	112-116	5	9
α-helix	119-121	3
β-strand	122	1	10
α-helix	123-124	2
β-strand	125-129	5	11
α-helix	130-132	3
β-strand	140-150	11	11
β-strand	151	1	10
β-strand	156-159	4	12
α-helix	160-162	3
β-strand	164	1	12
β-strand	168-170	3	11
α-helix	171-173	3
β-strand	174-176	3	11
β-strand	179-189	11	11
β-strand	199-204	6	12
α-helix	205-207	3
β-strand	209-214	6	12

Chain C: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	15	1	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab 5G12 light chain	A	protein	219	Mus musculus
Fab 5G12 heavy chain	B	protein	223	Mus musculus
Interleukin-21 receptor	C	protein	37	Homo sapiens	Q9HBE5 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6PLH_1 Fab 5G12 light chain (chains A)
DVVMTHTPLSLPVSLGDQASISCRSSQSLVHSNGNTYLHWYLQKPGQSPKLLIYKVSNRF
SGVPDRFSGSGSGADFTLKISRVEAEDLGVYFCSQSTHVPRTFGGGTKLEIKRADAAPTV
SIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSM
SSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 2 (B), FASTA

>6PLH_2 Fab 5G12 heavy chain (chains B)
QVHLQQPGADLVKPGASVKMSCKASGYTFTSYWITWVKLRPGQGLEWIGDIYPGSGSTNF
IEKFKSKATLTVDTSSSTAYMQLRSLTSEDSAVYYCARRGHGNYEDYWGQGTTLIVSSAK
TTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLY
TLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRGPTIK

Sequence of entity 3 (C), FASTA

>6PLH_3 Interleukin-21 receptor (chains C)
AGPMPGSSYQGTWSEWSDPVIFQTQSEELKEHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
MAN	alpha-D-mannopyranose	C6 H12 O6	1
PO4	Phosphate ion	O4 P	1

Primary citation

Yeast- and antibody-based tools for studying tryptophan C-mannosylation. John, A., Jarva, M.A., Shah, S. et al. Nat Chem Biol (2021) 17:428-437. DOI 10.1038/s41589-020-00727-w · PubMed

Other PDB entries of the same protein (UniProt Q9HBE5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7KQ7 2.2 Å, Crystal structure of IL21R in complex with an antibody Fab fragment
9E2T 2.28 Å, Structure of a de novo designed interleukin-21 mimetic complex with IL-21R and IL-2Rg
4NZD 2.75 Å, Interleukin 21 receptor
3TGX 2.8 Å, IL-21:IL21R complex
8ENT 2.83 Å, Interleukin-21 signaling complex with IL-21R and IL-2Rg

Browse structure collections

About this viewer

MolViewer shows 6PLH directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.