5M9W: Experimental MAD phased structure of thermolysin

Experimental MAD phased structure of thermolysin in complex with inhibitor JC65. Determined by X-ray diffraction at 1.21 Å resolution. Released 16 Aug 2017.

Method: X-ray diffraction
Resolution: 1.21 Å
Organism: Bacillus thermoproteolyticus
Chains: 1
Atoms: 2,941
Mol. weight: 35.5 kDa
Ligands: 7GR, CA, ZN
Released: 16 Aug 2017

Explore 5M9W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5M9W contains 13 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 A: 13 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
β-strand	56-57	2	1
β-strand	61-62	2	1
α-helix	65-67	3
α-helix	68-88	21
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	260-269	10
α-helix	270-274	5
α-helix	281-296	16
α-helix	301-312	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Thermolysin	A	protein	316	Bacillus thermoproteolyticus	P00800 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5M9W_1 Thermolysin (chains A)
ITGTSTVGVGRGVLGDQKNINTTYSTYYYLQDNTRGNGIFTYDAKYRTTLPGSLWADADN
QFFASYDAPAVDAHYYAGVTYDYYKNVHNRLSYDGNNAAIRSSVHYSQGYNNAFWNGSQM
VYGDGDGQTFIPLSGGIDVVAHELTHAVTDYTAGLIYQNESGAINEAISDIFGTLVEFYA
NKNPDWEIGEDVYTPGISGDSLRSMSDPAKYGDPDHYSKRYTGTQDNGGVHINSGIINKA
AYLISQGGTHYGVSVVGIGRDKLGKIFYRALTQYLTPTSNFSQLRAAAVQSATDLYGSTS
QEVASVKQAFDAVGVK

Ligands and cofactors

ID	Name	Formula	Copies
7GR	(2~{S})-4-methyl-2-[2-[[oxidanyl(phenylmethoxycarbonylaminomethyl)phosphoryl]am…	C17 H26 N3 O7 P	1
CA	Calcium ion	Ca	4
ZN	Zinc ion	Zn	1

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

Primary citation

How Nothing Boosts Affinity: Hydrophobic Ligand Binding to the Virtually Vacated S1' Pocket of Thermolysin. Krimmer, S.G., Cramer, J., Schiebel, J. et al. J Am Chem Soc (2017) 139:10419-10431. DOI 10.1021/jacs.7b05028 · PubMed

Other PDB entries of the same protein (UniProt P00800 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5JVI 1.12 Å, Thermolysin in complex with JC148.
5N3V 1.12 Å, Thermolysin in complex with inhibitor JC292
4N4E 1.13 Å, Thermolysin in complex with UBTLN58
5JS3 1.16 Å, Thermolysin in complex with JC114.
4MZN 1.17 Å, Thermolysin in complex with UBTLN59
5JSS 1.19 Å, Thermolysin in complex with JC149.
3DNZ 1.2 Å, Thermolysin by LB nanotemplate method before high X-Ray dose on ESRF ID14-2 beamline
5FSJ 1.2 Å, Structure of thermolysin prepared by the 'soak-and-freeze' method under 45 bar of oxygen…
5N2X 1.21 Å, Thermolysin in complex with inhibitor JC272
3DO2 1.22 Å, Thermolysin by LB nanotemplate method after high X-Ray dose on ESRF ID14-2 beamline
5N34 1.22 Å, Thermolysin in complex with inhibitor JC276
4MWP 1.23 Å, Thermolysin in complex with UBTLN46

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