6F60: Bovine pancreatic ribonuclease

The x-ray structure of bovine pancreatic ribonuclease in complex with a five-coordinate platinum(II) compound containing a sugar ligand. Determined by X-ray diffraction at 1.14 Å resolution. Released 25 Apr 2018.

Method: X-ray diffraction
Resolution: 1.14 Å
Organism: Bos taurus
Chains: 2
Atoms: 2,774
Mol. weight: 28.69 kDa
Ligands: DW5, DVW
Released: 25 Apr 2018

Explore 6F60 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6F60 contains 8 α-helices and 20 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.

Chains A and B: 4 helices, 10 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	51-55	5
α-helix	56-59	4
β-strand	61-63	3	2
β-strand	72-74	3	2
β-strand	79-86	8	1
β-strand	91	1	3
β-strand	94	1	3
β-strand	97-104	8	1
β-strand	106-111	6	2
β-strand	116-123	8	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ribonuclease pancreatic	A, B	protein	124	Bos taurus	P61823 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6F60_1 Ribonuclease pancreatic (chains A, B)
KETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQ
KNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNPYVPVHF
DASV

Ligands and cofactors

ID	Name	Formula	Copies
DW5	five-coordinate platinum(II) compound	C17 H19 N2 Pt	1
DVW	five-coordinate platinum(II) compound	C27 H31 N7 O5 Pt	1

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

Primary citation

Five-Coordinate Platinum(II) Compounds Containing Sugar Ligands: Synthesis, Characterization, Cytotoxic Activity, and Interaction with Biological Macromolecules. Cucciolito, M.E., D'Amora, A., De Feo, G. et al. Inorg Chem (2018) 57:3133-3143. DOI 10.1021/acs.inorgchem.7b03118 · 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…
1DY5 0.87 Å, Deamidated derivative of bovine pancreatic ribonuclease
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

Browse structure collections

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