1X1Y: Ribonuclease

Water-mediate interaction at aprotein-protein interface. Determined by X-ray diffraction at 1.9 Å resolution. Released 26 Apr 2005.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Bacillus amyloliquefaciens
Chains: 6
Atoms: 5,321
Mol. weight: 67.76 kDa
Released: 26 Apr 2005

Explore 1X1Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1X1Y contains 28 α-helices and 30 β-strands across 6 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, 7 β-strands

Element	Residues	Length	Sheet
α-helix	7-17	11
β-strand	24-25	2	1
α-helix	27-32	6
α-helix	37-39	3
α-helix	42-45	4
β-strand	50-51	2	1
β-strand	52-56	5	2
β-strand	71-75	5	2
β-strand	87-91	5	2
β-strand	96-99	4	2
β-strand	107-108	2	2

Chain B: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	7-17	11
β-strand	24-25	2	3
α-helix	27-33	7
α-helix	37-39	3
α-helix	42-45	4
β-strand	50-51	2	3
β-strand	52-56	5	4
α-helix	64-65	2
β-strand	71-75	5	4
β-strand	87-91	5	4
β-strand	96-99	4	4
β-strand	107-108	2	4

Chain D: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	1-6	6	7
α-helix	7-9	3
α-helix	13-23	11
α-helix	34-43	10
β-strand	49-54	6	7
α-helix	56-61	6
α-helix	66-79	14
β-strand	84-88	5	7

Chain E: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	8
α-helix	7-9	3
α-helix	13-24	12
α-helix	34-43	10
β-strand	49-54	6	8
α-helix	56-62	7
α-helix	66-79	14
β-strand	84-88	5	8

Chain F: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	9
α-helix	7-9	3
α-helix	13-23	11
α-helix	34-43	10
β-strand	49-54	6	9
α-helix	56-62	7
α-helix	66-80	15
β-strand	84-88	5	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ribonuclease	A, B, C	protein	110	Bacillus amyloliquefaciens	P00648 (AlphaFold model)
Barstar	D, E, F	protein	90	Bacillus amyloliquefaciens	P11540 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>1X1Y_1 Ribonuclease (chains A, B, C)
AAVINTFDGVADYLQTYHKLPDNYITKSEAQALGWVASKGNLADVAPGKSIGGDIFSNRE
GKLPGKSGRTWREADINYTSGFRNSDRILYSSDWLIYKTTDHYQTFTKIR

Sequence of entity 2 (D, E, F), FASTA

>1X1Y_2 Barstar (chains D, E, F)
MKKAVINGEQIRSISDLHQTLKKELALPEYYGENLAALWDALTGWVEYPLVLEWRQFEQS
KQLTENGAESVLQVFREAKAEGADITIILS

Primary citation

Water-mediated interaction at a protein-protein interface. Ikura, T., Urakubo, Y., Ito, N. Chem Phys (2004) 307:111-119. PubMed

Other PDB entries of the same protein (UniProt P00648 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6PQK 1.2 Å, Cryogenic crystal structure of barnase A43C/S80C bound to barstar C40A/S59C/A67C/C82A
2C4B 1.3 Å, Inhibitor cystine knot protein McoEeTI fused to the catalytically inactive barnase…
1A2P 1.5 Å, Barnase wildtype structure at 1.5 Å resolution
2ZA4 1.58 Å, Crystal Structural Analysis of Barnase-barstar Complex
1B20 1.7 Å, Deletion of a buried salt-bridge in barnase
1BRN 1.76 Å, Subsite binding in an RNase: structure of a barnase-tetranucleotide complex at 1.76 Å…
1B2X 1.8 Å, Barnase wildtype structure at PH 7.5 from a cryo_cooled crystal at 100K
1B2S 1.82 Å, Structural response to mutation at a protein-protein interface
1BRI 1.9 Å, Barnase mutant with ile 76 replaced by ala
1RNB 1.9 Å, Crystal structure of a barnase-d(*gp*c) complex at 1.9 Å resolution
3KCH 1.94 Å, Baranase crosslinked by glutaraldehyde
2F5M 1.95 Å, Cross-linked barnase soaked in bromo-ethanol

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