5DDZ: RTA-c10-P2 complex

Crystal structure of the RTA-c10-P2 complex. Determined by X-ray diffraction at 1.5 Å resolution. Released 7 Sept 2016.

Method: X-ray diffraction
Resolution: 1.5 Å
Organisms: Ricinus communis, Homo sapiens
Chains: 2
Atoms: 2,319
Mol. weight: 32.09 kDa
Released: 7 Sept 2016

Explore 5DDZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5DDZ contains 17 α-helices and 15 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	8-12	5	1
α-helix	18-32	15
β-strand	38-39	2	2
β-strand	42-43	2	2
β-strand	44	1	3
α-helix	45-47	3
α-helix	53-55	3
β-strand	57-63	7	1
β-strand	69-75	7	1
β-strand	81-86	6	1
β-strand	89-92	4	1
α-helix	93-95	3
α-helix	98-104	7
β-strand	113-116	4	1
α-helix	123-130	8
α-helix	134-136	3
β-strand	139	1	4
α-helix	141-153	13
α-helix	154-156	3
α-helix	161-171	11
α-helix	172-177	6
α-helix	178-180	3
α-helix	182-193	12
β-strand	198	1	4
α-helix	202-219	18
β-strand	222	1	5
β-strand	225-233	9	5
β-strand	239-244	6	5
α-helix	245-248	4
β-strand	255	1	3
α-helix	260-262	3

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	112-114	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ricin	A	protein	275	Ricinus communis	P02879 (AlphaFold model)
60S acidic ribosomal protein P2	B	protein	10	Homo sapiens	P05387 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5DDZ_1 Ricin (chains A)
MGHHHHHHIFPKQYPIINFTTAGATVQSYTNFIRAVRGRLTTGADVRHEIPVLPNRVGLP
INQRFILVELSNHAELSVTLALDVTNAYVVGYRAGNSAYFFHPDNQEDAEAITHLFTDVQ
NRYTFAFGGNYDRLEQLAGNLRENIELGNGPLEEAISALYYYSTGGTQLPTLARSFIICI
QMISEAARFQYIEGEMRTRIRYNRRSAPDPSVITLENSWGRLSTAIQESNQGAFASPIQL
QRRNGSKFSVYDVSILIPIIALMVYRCAPPPSSQF

Sequence of entity 2 (B), FASTA

>5DDZ_2 60S acidic ribosomal protein P2 (chains B)
DDDMGFGLFD

Primary citation

Structural insights into the interaction of the ribosomal P stalk protein P2 with a type II ribosome-inactivating protein ricin. Fan, X., Zhu, Y., Wang, C. et al. Sci Rep (2016) 6:37803-37803. DOI 10.1038/srep37803 · PubMed

Other PDB entries of the same protein (UniProt P02879 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7Y07 1.25 Å, Crystal structure of Ricin A chain bound with (S)-2-amino-N-(1-hydroxy-3-phenylpropan-2-y…
7Y08 1.25 Å, Crystal structure of Ricin A chain bound with (2-amino-4-oxo-3,4-dihydropteridine-7-carbo…
3PX8 1.29 Å, RTA in complex with 7-carboxy-pterin
7XZT 1.3 Å, Crystal structure of Ricin A chain bound with (2-amino-4-oxo-3,4-dihydropteridine-7-carbo…
7TGF 1.35 Å, Single-domain VHH intrabodies neutralize ricin toxin.
7Y03 1.35 Å, Crystal structure of Ricin A chain bound with (S)-2-(2-amino-4-oxo-3,4-dihydropteridine-7…
7Y06 1.35 Å, Crystal structure of Ricin A chain bound with (S)-2-(2-amino-4-oxo-3,4-dihydropteridine-7…
2VC4 1.39 Å, Ricin A-Chain (Recombinant) E177D Mutant
1UQ5 1.4 Å, Ricin a-chain (recombinant) N122A mutant
7XZW 1.45 Å, Crystal structure of Ricin A chain bound with (2-amino-4-oxo-3,4-dihydropteridine-7-carbo…
7Y4M 1.45 Å, Crystal structure of Ricin A chain bound with N2-(2-amino-4-oxo-3,4-dihydropteridine-7-ca…
1J1M 1.5 Å, Ricin A-Chain (Recombinant) at 100K

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