1DY5: Ribonuclease A

Deamidated derivative of bovine pancreatic ribonuclease. Determined by X-ray diffraction at 0.87 Å resolution. Released 28 Mar 2000.

Method: X-ray diffraction
Resolution: 0.87 Å
Organism: BOS TAURUS
Chains: 2
Atoms: 2,468
Mol. weight: 28.42 kDa
Ligands: IPA
Released: 28 Mar 2000

Explore 1DY5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1DY5 contains 8 α-helices and 22 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: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	4-12	9
β-strand	13	1	1
α-helix	25-32	8
β-strand	43-47	5	1
α-helix	51-56	6
α-helix	57-59	3
β-strand	61-63	3	2
β-strand	72-74	3	2
β-strand	78	1	3
β-strand	79-86	8	1
β-strand	91	1	4
β-strand	94	1	4
β-strand	97-104	8	1
β-strand	106-111	6	2
β-strand	116-123	8	2

Chain B: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	3
α-helix	4-12	9
β-strand	13	1	5
α-helix	25-32	8
β-strand	43-47	5	5
α-helix	51-56	6
α-helix	57-59	3
β-strand	61-63	3	6
β-strand	72-74	3	6
β-strand	79-86	8	5
β-strand	91	1	7
β-strand	94	1	7
β-strand	97-104	8	5
β-strand	106-111	6	6
β-strand	116-123	8	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ribonuclease A	A, B	protein	124	BOS TAURUS	P61823 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>1DY5_1 RIBONUCLEASE A (chains A, B)
KETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQ
KNVACKDGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNPYVPVHF
DASV

Ligands and cofactors

ID	Name	Formula	Copies
IPA	Isopropyl alcohol	C3 H8 O	8

Water and common crystallization additives (SO4, ACT) are not listed.

Primary citation

The Ultrahigh Resolution Crystal Structure of Ribonuclease A Containing an Isoaspartyl Residue: Hydration and Sterochemical Analysis. Esposito, L., Vitagliano, L., Sica, F. et al. J Mol Biol (2000) 297:713. DOI 10.1006/JMBI.2000.3597 · PubMed

Other PDB entries of the same protein (UniProt P61823 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6ETK 0.85 Å, Atomic resolution structure of RNase A (data collection 1)
6ETL 0.85 Å, Atomic resolution structure of RNase A (data collection 2)
7P4R 0.85 Å, Ultra High Resolution X-ray Structure of Orthorhombic Bovine Pancreatic Ribonuclease at…
6ETM 0.92 Å, Atomic resolution structure of RNase A (data collection 3)
6ETN 0.92 Å, Atomic resolution structure of RNase A (data collection 4)
6ETO 1.02 Å, Atomic resolution structure of RNase A (data collection 5)
6ETP 1.02 Å, Atomic resolution structure of RNase A (data collection 6)
1KF3 1.05 Å, Atomic Resolution Structure of RNase A at pH 5.9
2E3W 1.05 Å, X-ray structure of native RNase A
6ETQ 1.08 Å, Atomic resolution structure of RNase A (data collection 7)
1KF2 1.1 Å, Atomic Resolution Structure of RNase A at pH 5.2
1KF4 1.1 Å, Atomic Resolution Structure of RNase A at pH 6.3

Browse structure collections

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