2WM3

Crystal structure of NmrA-like family domain containing protein 1 in complex with niflumic acid

PDB DOI: https://doi.org/10.2210/pdb2WM3/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-06-29 Released: 2009-08-04
Deposition Author(s): Bhatia, C., Yue, W.W., Niesen, F., Pilka, E., Ugochukwu, E., Savitsky, P., Hozjan, V., Roos, A.K., Filippakopoulos, P., von Delft, F., Heightman, T., Arrowsmith, C., Weigelt, J., Edwards, A., Bountra, C., Oppermann, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.197 (Depositor), 0.210 (DCC)
R-Value Work:
0.166 (Depositor), 0.190 (DCC)
R-Value Observed:
0.167 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Crystal Structure of Nmra-Like Family Domain Containing Protein 1 in Complex with Niflumic Acid

Bhatia, C., Yue, W.W., Pilka, E., Ugochukwu, E., Savitsky, P., Hozjan, V., Roos, A.K., Filippakopoulos, P., von Delft, F., Heightman, T., Arrowsmith, C., Weigelt, J., Edwards, A., Bountra, C., Oppermann, U.

To be published.

Macromolecule Content

Total Structure Weight: 34.89 kDa
Atom Count: 2,713
Modelled Residue Count: 296
Deposited Residue Count: 299
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NMRA-LIKE FAMILY DOMAIN CONTAINING PROTEIN 1	A	299	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HBL8 (Homo sapiens) Explore Q9HBL8 Go to UniProtKB: Q9HBL8
PHAROS: Q9HBL8 GTEx: ENSG00000153406
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9HBL8
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
NFL Query on NFL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	2-{[3-(TRIFLUOROMETHYL)PHENYL]AMINO}NICOTINIC ACID C₁₃ H₉ F₃ N₂ O₂ JZFPYUNJRRFVQU-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.197 (Depositor), 0.210 (DCC)
R-Value Work: 0.166 (Depositor), 0.190 (DCC)
R-Value Observed: 0.167 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.712	α = 90
b = 68.712	β = 90
c = 183.789	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-08-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-08-04
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2012-12-05
Changes: Database references, Non-polymer description, Other, Source and taxonomy, Structure summary
Version 1.3: 2018-01-24
Changes: Database references
Version 1.4: 2024-05-08
Changes: Data collection, Database references, Derived calculations, Other