4MTZ | pdb_00004mtz

Structure of XIAP-BIR1 in complex with NF023

PDB DOI: https://doi.org/10.2210/pdb4MTZ/pdb

Classification: LIGASE/LIGASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-09-20 Released: 2014-09-24
Deposition Author(s): Cossu, F., Milani, M., Grassi, S., Mastrangelo, E., Bolognesi, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.242 (Depositor), 0.250 (DCC)
R-Value Work:
0.190 (Depositor), 0.199 (DCC)
R-Value Observed:
0.193 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Protein-protein interactions in nfkb pathway: novel tools to promote apoptosis in cancer therapy

Cossu, F., Milani, M., Grassi, S., Malvezzi, F., Corti, A., Bolognesi, M., Mastrangelo, E.

To be published.

Macromolecule Content

Total Structure Weight: 51.85 kDa
Atom Count: 2,737
Modeled Residue Count: 309
Deposited Residue Count: 444
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase XIAP	A, B, C, D	111	Homo sapiens	Mutation(s): 0 Gene Names: XIAP, API3, BIRC4, IAP3 EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P98170 (Homo sapiens) Explore P98170 Go to UniProtKB: P98170
PHAROS: P98170 GTEx: ENSG00000101966
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P98170
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0BU Query on 0BU Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain I [auth C] MOL2 format, chain K [auth D] MOL2 format, chain I [auth C] mmCIF format, chain K [auth D] mmCIF format, chain I [auth C]	I [auth C], K [auth D]	8-({3-[({3-[(4,6,8-trisulfonaphthalen-1-yl)carbamoyl]phenyl}carbamoyl)amino]benzoyl}amino)naphthalene-1,3,5-trisulfonic acid C₃₅ H₂₆ N₄ O₂₁ S₆ JMONOAYAUIIKMS-UHFFFAOYSA-N		Interactions Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain I [auth C] Focus chain K [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain J [auth D] SDF format, chain H [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain J [auth D] MOL2 format, chain H [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain J [auth D] mmCIF format, chain H [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], H [auth C], J [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain H [auth C] Focus chain J [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain H [auth C] Focus chain J [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.242 (Depositor), 0.250 (DCC)
R-Value Work: 0.190 (Depositor), 0.199 (DCC)
R-Value Observed: 0.193 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.854	α = 90
b = 76.209	β = 90
c = 71.191	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-09-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-09-24
Type: Initial release
Version 1.1: 2020-01-29
Changes: Advisory, Database references, Derived calculations
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-11-27
Changes: Structure summary

4MTZ | pdb_00004mtz

Structure of XIAP-BIR1 in complex with NF023

Literature

Protein-protein interactions in nfkb pathway: novel tools to promote apoptosis in cancer therapy

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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