RCSB PDB - 3K3L: Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with apo Enterobactin (original) (raw)
3K3L | pdb_00003k3l
Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with apo Enterobactin
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: 63.59 kDa
- Atom Count: 3,940
- Modelled Residue Count: 504
- Deposited Residue Count: 534
- Unique protein chains: 1
Find similar proteins by:
(by identity cutoff) | 3D Structure
| Ligands 7 Unique | ||||
|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions |
| MCKQuery on MCKDownload Ideal Coordinates CCD File | K [auth C] | N-[(2,3-dihydroxyphenyl)carbonyl]-O-[(2S)-2-{[(2,3-dihydroxyphenyl)carbonyl]amino}-3-(L-seryloxy)propanoyl]-L-serineC23 H25 N3 O13AVZOYWMPRGKOPV-IHRRRGAJSA-N |  |
Interactions Interactions & Density |
| DBSQuery on DBSDownload Ideal Coordinates CCD File | D [auth A] | 2-(2,3-DIHYDROXY-BENZOYLAMINO)-3-HYDROXY-PROPIONIC ACIDC10 H11 N O6VDTYHTVHFIIEIL-LURJTMIESA-N |  |
Interactions Interactions & Density |
| DBHQuery on DBHDownload Ideal Coordinates CCD File | E [auth A],F [auth A] | 2,3-DIHYDROXY-BENZOIC ACIDC7 H6 O4GLDQAMYCGOIJDV-UHFFFAOYSA-N |  |
Interactions Interactions & Density |
| SO4Query on SO4Download Ideal Coordinates CCD File | J [auth A] | SULFATE IONO4 SQAOWNCQODCNURD-UHFFFAOYSA-L |  |
Interactions Interactions & Density |
| GOLQuery on GOLDownload Ideal Coordinates CCD File | G [auth A]H [auth A]L [auth C]M [auth C]N [auth C]G [auth A],H [auth A],L [auth C],M [auth C],N [auth C],O [auth C],P [auth C] | GLYCEROLC3 H8 O3PEDCQBHIVMGVHV-UHFFFAOYSA-N |  |
Interactions Interactions & Density |
| CLQuery on CLDownload Ideal Coordinates CCD File | R [auth C] | CHLORIDE IONClVEXZGXHMUGYJMC-UHFFFAOYSA-M |  |
Interactions Interactions & Density |
| NAQuery on NADownload Ideal Coordinates CCD File | I [auth A],Q [auth C] | SODIUM IONNaFKNQFGJONOIPTF-UHFFFAOYSA-N |  |
Interactions Interactions & Density |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.62 Å
- R-Value Free: 0.307 (Depositor), 0.300 (DCC)
- R-Value Work: 0.260 (Depositor), 0.260 (DCC)
- R-Value Observed: 0.264 (Depositor)
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 114.2 | α = 90 |
| b = 114.2 | β = 90 |
| c = 119.3 | γ = 90 |
Software Package:
| Software Name | Purpose |
|---|---|
| HKL-2000 | data collection |
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| REFMAC | phasing |
Deposition Data
- Released Date: 2010-08-18 Deposition Author(s): [Clifton, M.C.](/search?q=audit%5Fauthor.name:Clifton, M.C.)
Revision History (Full details and data files)
- Version 1.0: 2010-08-18
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2019-02-27
Changes: Data collection, Database references - Version 1.3: 2021-10-13
Changes: Database references, Derived calculations - Version 1.4: 2024-10-09
Changes: Data collection, Structure summary