8ZVX | pdb_00008zvx

Crystal structure of snFPITE-n2

PDB DOI: https://doi.org/10.2210/pdb8ZVX/pdb

Classification: BLOOD CLOTTING
Organism(s): Sipunculus nudus
Expression System: Sipunculus nudus
Mutation(s): No

Deposited: 2024-06-12 Released: 2025-04-02
Deposition Author(s): Chen, X., Yang, H.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 ?
R-Value Free:
0.186 (Depositor), 0.189 (DCC)
R-Value Work:
0.163 (Depositor), 0.166 (DCC)
R-Value Observed:
0.164 (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

A Novel Facultative Plasminogen Independent Thrombolytic Enzyme Pool in the Ancient Peanut Worm (Sipunculus nudus)

Ma, G.X., Tang, M.Q., Xu, C.Y., Lin, H.J., Yang, H., Bian, C., Lu, M.L., Xiao, L.H., Hu, B., Chen, L., Hu, C.J., Li, Z.F., Cai, S.F., Wu, Y.Q., Li, W.H., Sun, Y.C., Yang, K., Yan, H., Xiong, Y.N., Zhao, Y.G., Lv, Z.M., Xu, X.M., Liu, C., Xin, P.L., Ye, L.C., Cui, X.L., Shi, Q., Chen, X., Xu, R.A.

To be published.

Macromolecule Content

Total Structure Weight: 51.37 kDa
Atom Count: 4,045
Modelled Residue Count: 478
Deposited Residue Count: 478
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
snFPITE-n2 A chain	A	239	Sipunculus nudus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
snFPITE-n2 B chain	B	239	Sipunculus nudus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B] mmCIF format, chain M [auth B]	M [auth B]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]
PMS Query on PMS Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain I [auth B]	C [auth A], I [auth B]	phenylmethanesulfonic acid C₇ H₈ O₃ S NIXKBAZVOQAHGC-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	D [auth A], E [auth A], J [auth B], K [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B]	F [auth A], G [auth A], H [auth A], L [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B]