7AM6: Peptiligase mutant - L217H/M222P/A225N/F189W

Name: PDB 7AM6: Crystal structure of Peptiligase mutant - L217H/M222P/A225N/F189W
Published: 2021-02-17
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Crystal structure of Peptiligase mutant - L217H/M222P/A225N/F189W. Determined by X-ray diffraction at 2.7 Å resolution. Released 17 Feb 2021.

Method: X-ray diffraction
Resolution: 2.7 Å
Organisms: Bacillus amyloliquefaciens, Hirudo medicinalis
Chains: 4
Atoms: 5,841
Mol. weight: 85.05 kDa
Ligands: TAR
Released: 17 Feb 2021

Explore 7AM6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7AM6 contains 37 α-helices and 53 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.

Chain A: 13 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
α-helix	14-18	5
β-strand	27-32	6	1
β-strand	44-49	6	1
α-helix	64-75	12
β-strand	89-94	6	1
α-helix	104-116	13
β-strand	121-124	4	1
β-strand	128	1	2
α-helix	133-145	13
β-strand	148-152	5	1
β-strand	159	1	3
β-strand	161-162	2	3
α-helix	165-166	2
β-strand	167	1	2
β-strand	175-180	6	1
α-helix	185	1
β-strand	186	1	1
α-helix	187	1
β-strand	198-201	4	1
β-strand	205-209	5	4
β-strand	213-217	5	4
α-helix	220-237	18
α-helix	243-252	10
β-strand	255	1	1
α-helix	256	1
α-helix	260-263	4
β-strand	267	1	1
α-helix	270-273	4

Chain B: 12 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
α-helix	14-17	4
β-strand	27-32	6	5
β-strand	44-49	6	5
α-helix	64-75	12
β-strand	89-94	6	5
β-strand	101	1	6
α-helix	104-116	13
β-strand	121-124	4	5
β-strand	127	1	6
β-strand	128	1	7
α-helix	133-145	13
β-strand	148-152	5	5
β-strand	159	1	8
β-strand	161	1	8
α-helix	165-166	2
β-strand	167	1	7
β-strand	175-180	6	5
α-helix	185	1
β-strand	186	1	5
α-helix	187	1
β-strand	198-201	4	5
β-strand	205-209	5	9
β-strand	213-217	5	9
α-helix	220-237	18
α-helix	243-252	10
β-strand	255	1	5
α-helix	260-263	4
β-strand	267	1	5
α-helix	270-273	4

Chain C: 12 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	6-10	5
α-helix	14-18	5
β-strand	27-32	6	10
β-strand	44-49	6	10
α-helix	64-75	12
β-strand	89-94	6	10
α-helix	104-116	13
β-strand	121-124	4	10
β-strand	126-127	2	11
β-strand	128	1	12
α-helix	133-145	13
β-strand	148-152	5	10
β-strand	159	1	13
β-strand	161-162	2	13
α-helix	165-166	2
β-strand	167	1	12
β-strand	175-180	6	10
α-helix	185	1
β-strand	186	1	10
α-helix	187	1
β-strand	196-201	6	10
β-strand	205	1	14
β-strand	211	1	6
β-strand	217	1	14
α-helix	220-237	18
α-helix	243-252	10
β-strand	255	1	10
α-helix	260-263	4
β-strand	267	1	10
α-helix	270-273	4

Chain P: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	43-44	2	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Subtilisin BPN'	A, C	protein	272	Bacillus amyloliquefaciens	P00782 (AlphaFold model)
Subtilisin BPN'	B	protein	272	Bacillus amyloliquefaciens	P00782 (AlphaFold model)
Leu-pro-glu-gly-ser-pro-val-thr-asp-leu-arg-tyr	P	protein	13	Hirudo medicinalis	P01051 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>7AM6_1 Subtilisin BPN' (chains A, C)
AKCVSYGVSQIKAPALHSQGYTGSNVKVAVIDSGIDSSHPDLNVAGGASFVPSETNPFQD
NNSHGTHVAGTVLAVAPSASLYAVKVLGADGSGQYSWIINGIEWAIANNMDVINMSLGGP
SGSAALKAAVDKAVASGVVVVAAAGNSGTSGSSSTVSYPAKYPSVIAVGAVDSSNQRAPW
SSVGPELDVMAPGVSICSTLPGNKYGAHSGTCPASNHVAGAAALILSKHPNWTNTQVRSS
LENTATKLGDSFYYGKGLINVEAAAQHHHHHH

Sequence of entity 2 (B), FASTA

>7AM6_2 Subtilisin BPN' (chains B)
AKCVSYGVSQIKAPALHSQGYTGSNVKVAVIDSGIDSSHPDLNVAGGASFVPSETNPFQD
NNSHGTHVAGTVLAVAPSASLYAVKVLGADGSGQYSWIINGIEWAIANNMDVINMSLGGP
SGSAALKAAVDKAVASGVVVVAAAGNSGTSGSSSTVSYPAKYPSVIAVGAVDSSNQRAPW
SSVGPELDVMAPGVSICSTLPGNKYGAHSGTCPASNHVAGAAALILSKHPNWTNTQVRSS
LENTATKLGDSFYYGKGLINVEAAAQHHHHHH

Sequence of entity 3 (P), FASTA

>7AM6_3 LEU-PRO-GLU-GLY-SER-PRO-VAL-THR-ASP-LEU-ARG-TYR (chains P)
LPEGSPVTLDLRY

Ligands and cofactors

ID	Name	Formula	Copies
TAR	D(-)-tartaric acid	C4 H6 O6	2

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

Primary citation

From thiol-subtilisin to omniligase: Design and structure of a broadly applicable peptide ligase. Toplak, A., Teixeira de Oliveira, E.F., Schmidt, M. et al. Comput Struct Biotechnol J (2021) 19:1277-1287. DOI 10.1016/j.csbj.2021.02.002 · PubMed

Other PDB entries of the same protein (UniProt P00782 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1TO2 1.3 Å, crystal structure of the complex of subtilisin BPN' with chymotrypsin inhibitor 2 M59K,…
1TM5 1.45 Å, crystal structure of the complex of subtilisin BPN' with chymotrypsin inhibitor 2 M59A…
1LW6 1.5 Å, Crystal Structure of the Complex of Subtilisin BPN' with Chymotrypsin Inhibitor 2 at 1.5…
1V5I 1.5 Å, Crystal structure of serine protease inhibitor POIA1 in complex with subtilisin BPN'
1Y34 1.55 Å, Crystal structure of the complex of subtilisin BPN' with chymotrypsin inhibitor 2 E60A…
8H7O 1.55 Å, Crystal structure of aqualigase
1Y1K 1.56 Å, Crystal structure of the complex of subtilisin BPN' with chymotrypsin inhibitor 2 T58A…
1TM3 1.57 Å, crystal structure of the complex of subtilisin BPN' with chymotrypsin inhibitor 2 M59k…
1TM7 1.59 Å, crystal structure of the complex of subtilisin BPN' with chymotrypsin inhibitor 2 M59Y…
1SUP 1.6 Å, Subtilisin bpn' at 1.6 Å resolution: analysis of discrete disorder and comparison of…
1Y4A 1.6 Å, Crystal structure of the complex of subtilisin BPN' with chymotrypsin inhibitor 2…
7AM3 1.61 Å, Crystal structure of Peptiligase mutant - M222P

Browse structure collections

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