RCSB PDB - 3TZS: Crystal structure of Neutrophil gelatinase-associated lipocalin NGAL (C87S mutant) in complex with fragment 1026, phenylurea (original) (raw)
3TZS | pdb_00003tzs
Crystal structure of Neutrophil gelatinase-associated lipocalin NGAL (C87S mutant) in complex with fragment 1026, phenylurea
This is version 1.4 of the entry. See complete history.
Parsing the functional specificity of Siderocalin / Lipocalin 2 / NGAL for siderophores and related small-molecule ligands
[Clifton, M.C.](/search?q=citation.rcsb%5Fauthors:Clifton, M.C.), [Rupert, P.B.](/search?q=citation.rcsb%5Fauthors:Rupert, P.B.), [Hoette, T.M.](/search?q=citation.rcsb%5Fauthors:Hoette, T.M.), [Raymond, K.N.](/search?q=citation.rcsb%5Fauthors:Raymond, K.N.), [Abergel, R.J.](/search?q=citation.rcsb%5Fauthors:Abergel, R.J.), [Strong, R.K.](/search?q=citation.rcsb%5Fauthors:Strong, R.K.)
To be published.
Macromolecule Content
- Total Structure Weight: 64.81 kDa
- Atom Count: 4,356
- Modelled Residue Count: 520
- Deposited Residue Count: 549
- Unique protein chains: 1
Find similar proteins by:
(by identity cutoff) | 3D Structure
| Ligands 4 Unique | ||||
|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions |
| PHUQuery on PHUDownload Ideal Coordinates CCD File | D [auth A],H [auth A],J [auth B],N [auth C],S [auth C] | 1-phenylureaC7 H8 N2 OLUBJCRLGQSPQNN-UHFFFAOYSA-N |  |
Interactions Interactions & Density |
| SO4Query on SO4Download Ideal Coordinates CCD File | E [auth A]G [auth A]K [auth B]M [auth B]O [auth C]E [auth A],G [auth A],K [auth B],M [auth B],O [auth C],R [auth C],T [auth C],U [auth C] | SULFATE IONO4 SQAOWNCQODCNURD-UHFFFAOYSA-L |  |
Interactions Interactions & Density |
| EDOQuery on EDODownload Ideal Coordinates CCD File | I [auth A],P [auth C] | 1,2-ETHANEDIOLC2 H6 O2LYCAIKOWRPUZTN-UHFFFAOYSA-N |  |
Interactions Interactions & Density |
| CLQuery on CLDownload Ideal Coordinates CCD File | F [auth A],L [auth B],Q [auth C] | CHLORIDE IONClVEXZGXHMUGYJMC-UHFFFAOYSA-M |  |
Interactions Interactions & Density |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.45 Å
- R-Value Free: 0.225 (Depositor), 0.220 (DCC)
- R-Value Work: 0.187 (Depositor), 0.190 (DCC)
- R-Value Observed: 0.189 (Depositor)
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 115.35 | α = 90 |
| b = 115.35 | β = 90 |
| c = 119.89 | γ = 90 |
Software Package:
| Software Name | Purpose |
|---|---|
| XSCALE | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| PHASER | phasing |
Revision History (Full details and data files)
- Version 1.0: 2011-10-12
Type: Initial release - Version 1.1: 2013-10-09
Changes: Database references - Version 1.2: 2019-02-13
Changes: Data collection, Database references - Version 1.3: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description - Version 1.4: 2024-10-09
Changes: Structure summary