9DIE | pdb_00009die

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

PDB DOI: https://doi.org/10.2210/pdb9DIE/pdb

Classification: LYASE
Organism(s): Sicarius terrosus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-09-05 Released: 2025-09-10
Deposition Author(s): Sundman, A.K., Montfort, W.R., Binford, G.J., Cordes, M.H.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.167 (Depositor), 0.178 (DCC)
R-Value Work:
0.119 (Depositor), 0.149 (DCC)
R-Value Observed:
0.121 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

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

Sundman, A.K., Montfort, W.R., Binford, G.J., Cordes, M.H.

To be published.

Macromolecule Content

Total Structure Weight: 72.32 kDa
Atom Count: 5,866
Modeled Residue Count: 556
Deposited Residue Count: 602
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dermonecrotic toxin StSicTox-betaIB1i	A, B	301	Sicarius terrosus	Mutation(s): 1 EC: 4.6.1
UniProt
Find proteins for A0A0D4WV12 (Sicarius terrosus) Explore A0A0D4WV12 Go to UniProtKB: A0A0D4WV12
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0D4WV12
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1A43 (Subject of Investigation/LOI) Query on A1A43 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	C [auth A], D [auth A], K [auth B], L [auth B]	2-aminoethyl (2S,3R,4E)-2-dodecanamido-3-hydroxyheptadec-4-en-1-yl hydrogen (S)-phosphate C₃₁ H₆₃ N₂ O₆ P ZIEWVPJUBVRCAL-DQBIDPIGSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain K [auth B] Focus chain L [auth B]
A1A44 (Subject of Investigation/LOI) Query on A1A44 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain M [auth B] MOL2 format, chain E [auth A] MOL2 format, chain M [auth B] mmCIF format, chain E [auth A] mmCIF format, chain M [auth B]	E [auth A], M [auth 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 C₂₉ H₅₆ N O₅ P WCWADZSYRHRKHD-LVDQGNEYSA-N		Interactions Focus chain E [auth A] Focus chain M [auth B] Interactions & Density Focus chain E [auth A] Focus chain M [auth B]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A]	I [auth A], J [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain P [auth B] MOL2 format, chain H [auth A] MOL2 format, chain P [auth B] mmCIF format, chain H [auth A] mmCIF format, chain P [auth B]	H [auth A], P [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain P [auth B] Interactions & Density Focus chain H [auth A] Focus chain P [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B]	F [auth A], G [auth A], N [auth B], O [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain N [auth B] Focus chain O [auth B]