RCSB PDB - 3TF6: Crystal structure of Neutrophil gelatinase-associated lipocalin (C87S mutant) in complex with Europium and the siderophore analog tren(cam)(1,2-hopo)2 (original) (raw)
3TF6 | pdb_00003tf6
Crystal structure of Neutrophil gelatinase-associated lipocalin (C87S mutant) in complex with Europium and the siderophore analog tren(cam)(1,2-hopo)2
This is version 1.3 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: 63.59 kDa
- Atom Count: 4,300
- Modelled Residue Count: 520
- Deposited Residue Count: 537
- Unique protein chains: 1
Find similar proteins by:
(by identity cutoff) | 3D Structure
| Ligands 5 Unique | ||||
|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions |
| DBHQuery on DBHDownload Ideal Coordinates CCD File | F [auth A],J [auth B],O [auth C] | 2,3-DIHYDROXY-BENZOIC ACIDC7 H6 O4GLDQAMYCGOIJDV-UHFFFAOYSA-N |  |
Interactions Interactions & Density |
| EUQuery on EUDownload Ideal Coordinates CCD File | E [auth A],I [auth B],N [auth C] | EUROPIUM IONEuMGVUQZZTJGLWJV-UHFFFAOYSA-N |  |
Interactions Interactions & Density |
| SO4Query on SO4Download Ideal Coordinates CCD File | G [auth A],K [auth B],P [auth C] | SULFATE IONO4 SQAOWNCQODCNURD-UHFFFAOYSA-L |  |
Interactions Interactions & Density |
| GOLQuery on GOLDownload Ideal Coordinates CCD File | D [auth A],M [auth C],Q [auth C],R [auth C] | GLYCEROLC3 H8 O3PEDCQBHIVMGVHV-UHFFFAOYSA-N |  |
Interactions Interactions & Density |
| CLQuery on CLDownload Ideal Coordinates CCD File | H [auth A],L [auth B],S [auth C],T [auth C],U [auth C] | CHLORIDE IONClVEXZGXHMUGYJMC-UHFFFAOYSA-M |  |
Interactions Interactions & Density |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.35 Å
- R-Value Free: 0.216 (Depositor), 0.214 (DCC)
- R-Value Work: 0.191 (Depositor), 0.192 (DCC)
- R-Value Observed: 0.194 (Depositor)
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 114.09 | α = 90 |
| b = 114.09 | β = 90 |
| c = 118.19 | γ = 90 |
Software Package:
| Software Name | Purpose |
|---|---|
| XSCALE | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| ADSC | data collection |
| XDS | data reduction |
| REFMAC | phasing |
Revision History (Full details and data files)
- Version 1.0: 2011-09-07
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: 2024-11-27
Changes: Data collection, Database references, Derived calculations, Structure summary