6Y4I: Thermolysin

Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin. Determined by X-ray diffraction at 1.16 Å resolution. Released 31 Mar 2021.

Method: X-ray diffraction
Resolution: 1.16 Å
Organism: Geobacillus stearothermophilus
Chains: 1
Atoms: 2,919
Mol. weight: 35.55 kDa
Ligands: CA, ZN, 0PK, CS
Released: 31 Mar 2021

Explore 6Y4I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6Y4I contains 14 α-helices and 17 β-strands across 1 chain. 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 E: 14 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4-11	8	1
β-strand	17-25	9	1
β-strand	27-29	3	1
β-strand	31-32	2	2
β-strand	39-43	5	2
β-strand	53-54	2	2
α-helix	55	1
β-strand	56-57	2	1
β-strand	61-62	2	1
α-helix	65-67	3
α-helix	68-88	21
α-helix	98-99	2
β-strand	100-106	7	2
β-strand	113-115	3	2
β-strand	120-123	4	2
β-strand	130	1	3
α-helix	133-135	3
α-helix	137-151	15
α-helix	159-180	22
β-strand	187-188	2	4
β-strand	193	1	3
β-strand	203-204	2	4
α-helix	208-211	4
α-helix	217-219	3
α-helix	225-229	5
α-helix	234-246	13
β-strand	248-250	3	5
β-strand	253-255	3	5
α-helix	260-273	14
α-helix	281-296	16
α-helix	301-312	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Thermolysin	E	protein	316	Geobacillus stearothermophilus	P43133 (AlphaFold model)

Sequence of entity 1 (E), FASTA

>6Y4I_1 Thermolysin (chains E)
ITGTSTVGVGRGVLGDQKNINTTYSTYYYLQDNTRGNGIFTYDAKYRTTLPGSLWADADN
QFFASYDAPAVDAHYYAGVTYDYYKNVHNRLSYDGNNAAIRSSVHYSQGYNNAFWNGSQM
VYGDGDGQTFIPLSGGIDVVAHELTHAVTDYTAGLIYQNESGAINEAISDIFGTLVEFYA
NKNPDWEIGEDVYTPGISGDSLRSMSDPAKYGDPDHYSKRYTGTQDNGGVHINSGIINKA
AYLISQGGTHYGVSVVGIGRDKLGKIFYRALTQYLTPTSNFSQLRAAAVQSATDLYGSTS
QEVASVKQAFDAVGVK

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	4
ZN	Zinc ion	Zn	1
0PK	N-[(S)-[(1R)-1-{[(benzyloxy)carbonyl]amino}-2-phenylethyl](hydroxy)phosphoryl]-…	C25 H34 N3 O7 P	1
CS	Cesium ion	Cs	1

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

Primary citation

Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin. Kljajic, M., Gerber, H.-D., Heine, A. et al. To be published.

Other PDB entries of the same protein (UniProt P43133 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6GHX 1.16 Å, Alzheimer's Amyloid-Beta Peptide Fragment 31-35 in Complex with Cd-substituted Thermolysin
5ONQ 1.17 Å, Alzheimer's Amyloid-Beta Peptide Fragment 29-40 in Complex with Cd-substituted Thermolysin
6YMS 1.32 Å, Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin
5ONP 1.34 Å, Alzheimer's Amyloid-Beta Peptide Fragment 1-40 in Complex with Cd-substituted Thermolysin
6FSM 1.39 Å, Crystal structure of TCE-treated Thermolysin
6YI6 1.44 Å, Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin
6YMR 1.6 Å, Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin
9P17 1.66 Å, Thermolysin Room-Temperature In-Situ, Shipped
6FHP 1.7 Å, DAIP in complex with a C-terminal fragment of thermolysin
9P16 1.73 Å, Thermolysin Room-Temperature In-Situ, Grown On-Site
9OZY 1.75 Å, Gradient equilibration of hexagonal thermolysin to low salt over 15 minutes
5WR5 1.9 Å, Thermolysin, liganded form with cryo condition 1

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