2P4A: Ribonuclease pancreatic

X-ray structure of a camelid affinity matured single-domain vhh antibody fragment in complex with RNASE A. Determined by X-ray diffraction at 1.9 Å resolution. Released 28 Aug 2007.

Method: X-ray diffraction
Resolution: 1.9 Å
Organisms: Bos taurus, Camelus dromedarius
Chains: 4
Atoms: 4,112
Mol. weight: 53.27 kDa
Released: 28 Aug 2007

Explore 2P4A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2P4A contains 13 α-helices and 42 β-strands across 4 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 C: 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	51-56	6
α-helix	57-59	3
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

Chain B: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	4
β-strand	10-13	4	5
β-strand	18-25	8	4
β-strand	33-39	7	5
α-helix	44-45	2
β-strand	46-52	7	5
β-strand	59-60	2	5
β-strand	68-71	4	4
β-strand	78-83	6	4
α-helix	88-90	3
β-strand	92-98	7	5
α-helix	105-107	3
β-strand	110-111	2	5
β-strand	115-120	6	5

Chain D: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	10-13	4	5
β-strand	18-25	8	9
β-strand	33-39	7	5
β-strand	46-52	7	5
β-strand	59-60	2	5
β-strand	68-71	4	9
β-strand	78-83	6	9
α-helix	88-90	3
β-strand	92-98	7	5
α-helix	105-107	3
β-strand	110-111	2	5
β-strand	115-120	6	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ribonuclease pancreatic	A, C	protein	124	Bos taurus	P61823 (AlphaFold model)
Antibody cab-RN05	B, D	protein	121	Camelus dromedarius	A2KD57 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>2P4A_1 Ribonuclease pancreatic (chains A, C)
KETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQ
KNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNPYVPVHF
DASV

Sequence of entity 2 (B, D), FASTA

>2P4A_2 ANTIBODY CAB-RN05 (chains B, D)
QVQLVESGGGLVQAGGSLRLSCAASGYPWTYIYMGWFRQAPGKEREGVAAMDSGGGGTLY
ADSVKGRFTISRDKGKNTVYLQMDSLKPEDTATYYCAAGGDALVATRYGRWGQGTQVTVS
S

Primary citation

Exploring the capacity of minimalist protein interfaces: interface energetics and affinity maturation to picomolar KD of a single-domain antibody with a flat paratope. Koide, A., Tereshko, V., Uysal, S. et al. J Mol Biol (2007) 373:941-953. DOI 10.1016/j.jmb.2007.08.027 · 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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