2JDL: C-terminal region of acidic P2 ribosomal protein

Structure of C-terminal region of acidic P2 ribosomal protein complexed with trichosanthin. Determined by X-ray diffraction at 2.2 Å resolution. Released 5 Feb 2008.

Method: X-ray diffraction
Resolution: 2.2 Å
Organisms: TRICHOSANTHES KIRILOWII, HOMO SAPIENS
Chains: 4
Atoms: 4,245
Mol. weight: 56.8 kDa
Released: 5 Feb 2008

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

Secondary structure: helices and β-sheets

2JDL contains 30 α-helices and 30 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 A: 16 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	1
α-helix	11-23	13
β-strand	27-31	5	2
β-strand	34-37	4	2
α-helix	38	1
α-helix	43-45	3
β-strand	47-53	7	1
β-strand	59-65	7	1
β-strand	71-76	6	1
β-strand	79-82	4	1
α-helix	86-91	6
β-strand	101-104	4	1
α-helix	111-118	8
α-helix	122-124	3
β-strand	127	1	3
α-helix	129-140	12
α-helix	147-155	9
α-helix	156-160	5
α-helix	161-163	3
β-strand	164	1	4
α-helix	165-172	8
β-strand	179	1	3
α-helix	180-182	3
α-helix	183-190	8
α-helix	192-202	11
β-strand	208-216	9	5
β-strand	222-227	6	5
α-helix	231-234	4
β-strand	237	1	4
β-strand	240	1	2
α-helix	243-245	3

Chain B: 14 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	6
α-helix	11-22	12
β-strand	27-31	5	7
β-strand	34-37	4	7
α-helix	38	1
β-strand	47-53	7	6
β-strand	59-65	7	6
β-strand	70-76	7	6
β-strand	79-82	4	6
α-helix	86-91	6
β-strand	101-104	4	6
α-helix	111-118	8
α-helix	122-124	3
β-strand	127	1	8
α-helix	129-140	12
α-helix	147-155	9
α-helix	156-160	5
α-helix	161-163	3
β-strand	164	1	9
α-helix	165-173	9
β-strand	179	1	8
α-helix	180-182	3
α-helix	183-203	21
β-strand	208-216	9	10
β-strand	222-227	6	10
α-helix	231-235	5
β-strand	237	1	9
β-strand	240	1	7
α-helix	243-245	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ribosome-inactivating protein alpha-trichosanthin	A, B	protein	247	TRICHOSANTHES KIRILOWII	P09989 (AlphaFold model)
Acidic ribosomal protein P2	C, D	protein	11	HOMO SAPIENS	P05387 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2JDL_1 RIBOSOME-INACTIVATING PROTEIN ALPHA-TRICHOSANTHIN (chains A, B)
MVSFRLSGATSSSYGVFISNLRKALPNERKLYDIPLLRSSLPGSQRYALIHLTNYADETI
SVAIDVTNVYIMGYRAGDTSYFFNEASATEAAKYVFKDAMRKVTLPYSGNYERLQTAAGK
IRENIPLGLPALDSAITTLFYYNANSAASALMVLIQSTSEAARYKFIEQQIGKRVDKTFL
PSLAIISLENSWSALSKQIQIASTNNGQFESPVVLINAQNQRVTITNVDAGVVTSNIALL
LNRNNMA

Sequence of entity 2 (C, D), FASTA

>2JDL_2 ACIDIC RIBOSOMAL PROTEIN P2 (chains C, D)
SDDDMGFGLFD

Primary citation

The C-Terminal Fragment of the Ribosomal P Protein Complexed to Trichosanthin Reveals the Interaction between the Ribosome-Inactivating Protein and the Ribosome. Too, P.H., Ma, M.K., Mak, A.N. et al. Nucleic Acids Res (2009) 37:602. DOI 10.1093/NAR/GKN922 · PubMed

Other PDB entries of the same protein (UniProt P09989 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1MRJ 1.6 Å, Studies on crystal structures active center geometry and depurine mechanism of two…
1MRK 1.6 Å, Studies on crystal structures active center geometry and depurine mechanism of two…
1GIS 1.7 Å, A trichosanthin(tcs) MUTANT(E85Q) complex structure with…
1TCS 1.7 Å, Crystal structure of trichosanthin-NADPH complex at 1.7 Å resolution reveals active-site…
1GIU 1.8 Å, A trichosanthin(tcs) MUTANT(E85R) complex structure with adenine
1QD2 1.86 Å, Crystal structure of the complex of trichosanthin with adenine, obtained from…
1NLI 1.93 Å, Complex of [E160A-E189A] trichosanthin and adenine
1J4G 2.0 Å, crystal structure analysis of the trichosanthin delta C7
2JJR 2.3 Å, V232K, N236D-trichosanthin
2VS6 2.4 Å, K173A, R174A, K177A-trichosanthin

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