9DIE

Structure of phospholipase D BetaIB1i from Sicarius terrosus venom, H47N mutant bound to product and substrate sphingolipids at 1.85 A resolution

This is a non-PDB format compatible entry.

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A, B (A, B)	Dermonecrotic toxin StSicTox-betaIB1i	polymer	301	34262.3	2	UniProt (A0A0D4WV12) Pfam (PF13653)	Sicarius terrosus	Phospholipase D,PLD,Sphingomyelin phosphodiesterase D,SMD,SMase D,Sphingomyelinase D
2	C, D, K, L (A, B)	2-aminoethyl (2S,3R,4E)-2-dodecanamido-3-hydroxyheptadec-4-en-1-yl hydrogen (S)-phosphate	non-polymer		590.8	4	Chemie (A1A43)
3	E, M (A, B)	N-{(2S,4R,5S)-2-hydroxy-2-oxo-4-[(1E,7Z)-tetradeca-1,7-dien-1-yl]-1,3,2lambda~5~-dioxaphosphinan-5-yl}dodecanamide	non-polymer		529.7	2	Chemie (A1A44)
4	F, G, N, O (A, B)	SODIUM ION	non-polymer		23.0	4	Chemie (NA)
5	H, P (A, B)	MAGNESIUM ION	non-polymer		24.3	2	Chemie (MG)
6	I, J (A)	(4S)-2-METHYL-2,4-PENTANEDIOL	non-polymer		118.2	2	Chemie (MPD)
7	Q, R (A, B)	water	water		18.0	884	Chemie (HOH)

Sequence modifications

A, B: 0 - 278 (UniProt: A0A0D4WV12)

PDB	External Database	Details
Met -22	-	initiating methionine
Lys -21	-	expression tag
His -20	-	expression tag
His -19	-	expression tag
His -18	-	expression tag
His -17	-	expression tag
His -16	-	expression tag
His -15	-	expression tag
His -14	-	expression tag
His -13	-	expression tag
Gly -12	-	expression tag
Gly -11	-	expression tag
Leu -10	-	expression tag
Val -9	-	expression tag
Pro -8	-	expression tag
Arg -7	-	expression tag
Gly -6	-	expression tag
Ser -5	-	expression tag
His -4	-	expression tag
Gly -3	-	expression tag
Gly -2	-	expression tag
Ser -1	-	expression tag
Asn 47	His 48	engineered mutation

Contents of the asymmetric unit

Polymers	Number of chains	2
	Total formula weight	68524.7
Non-Polymers*	Number of molecules	14
	Total formula weight	3799.6
All*	Total formula weight	72324.3

*Water molecules are not included.