6PQK: Cryogenic crystal structure of barnase A43C/S80C

Cryogenic crystal structure of barnase A43C/S80C bound to barstar C40A/S59C/A67C/C82A. Determined by X-ray diffraction at 1.2 Å resolution. Released 15 Jul 2020.

Method: X-ray diffraction
Resolution: 1.2 Å
Organism: Bacillus amyloliquefaciens
Chains: 4
Atoms: 4,014
Mol. weight: 50.35 kDa
Ligands: PO4
Released: 15 Jul 2020

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

Secondary structure: helices and β-sheets

6PQK contains 18 α-helices and 20 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, 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, 3 β-strands

Element	Residues	Length	Sheet
β-strand	1-6	6	5
α-helix	7-9	3
α-helix	13-23	11
α-helix	34-43	10
β-strand	49-54	6	5
α-helix	56-60	5
α-helix	67-79	13
β-strand	84-88	5	5

Chain D: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	6
α-helix	7-9	3
α-helix	13-23	11
α-helix	34-43	10
β-strand	49-54	6	6
α-helix	56-60	5
α-helix	67-80	14
β-strand	84-88	5	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ribonuclease	A, C	protein	128	Bacillus amyloliquefaciens	P00648 (AlphaFold model)
Barstar	B, D	protein	90	Bacillus amyloliquefaciens	P11540 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>6PQK_1 Ribonuclease (chains A, C)
MGSSHHHHHHSQDPIEGRAQVINTFDGVADYLQTYHKLPDNYITKSEAQALGWVASKGNL
CDVAPGKSIGGDIFSNREGKLPGKSGRTWREADINYTCGFRNSDRILYSSDWLIYKTTDH
YQTFTKIR

Sequence of entity 2 (B, D), FASTA

>6PQK_2 Barstar (chains B, D)
MKKAVINGEQIRSISDLHQTLKKELALPEYYGENLDALWDALTGWVEYPLVLEWRQFEQC
KQLTENGCESVLQVFREAKAEGADITIILS

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	4

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

Primary citation

Targeting conformational entropy to modulate binding affinity. Caro, J.A., Djanto, V., Wand, A.J. To be published.

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

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
1X1Y 1.9 Å, Water-mediate interaction at aprotein-protein interface
3KCH 1.94 Å, Baranase crosslinked by glutaraldehyde
2F5M 1.95 Å, Cross-linked barnase soaked in bromo-ethanol

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