RCSB PDB - 3CMP: Crystal structure of Siderocalin (NGAL, Lipocalin 2) K125A mutant complexed with Ferric Enterobactin (original) (raw)
3CMP | pdb_00003cmp
Crystal structure of Siderocalin (NGAL, Lipocalin 2) K125A mutant complexed with Ferric Enterobactin
This is version 1.5 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: 70.16 kDa
- Atom Count: 4,170
- Modelled Residue Count: 516
- Deposited Residue Count: 594
- Unique protein chains: 1
Find similar proteins by:
(by identity cutoff) | 3D Structure
| Ligands 6 Unique | ||||
|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions |
| EB4Query on EB4Download Ideal Coordinates CCD File | H [auth A],U [auth C] | **N,N',N''-[(3S,7S,11S)-2,6,10-trioxo-1,5,9-trioxacyclododecane-3,7,11-triyl]tris(2,3-dihydroxybenzamide)**C30 H27 N3 O15SERBHKJMVBATSJ-BZSNNMDCSA-N |  |
Interactions Interactions & Density |
| DBHQuery on DBHDownload Ideal Coordinates CCD File | L [auth B],M [auth B] | 2,3-DIHYDROXY-BENZOIC ACIDC7 H6 O4GLDQAMYCGOIJDV-UHFFFAOYSA-N |  |
Interactions Interactions & Density |
| SO4Query on SO4Download Ideal Coordinates CCD File | F [auth A],G [auth A],T [auth C] | SULFATE IONO4 SQAOWNCQODCNURD-UHFFFAOYSA-L |  |
Interactions Interactions & Density |
| GOLQuery on GOLDownload Ideal Coordinates CCD File | I [auth A],V [auth C],W [auth C] | GLYCEROLC3 H8 O3PEDCQBHIVMGVHV-UHFFFAOYSA-N |  |
Interactions Interactions & Density |
| FEQuery on FEDownload Ideal Coordinates CCD File | D [auth A],J [auth B],N [auth C] | FE (III) IONFeVTLYFUHAOXGGBS-UHFFFAOYSA-N |  |
Interactions Interactions & Density |
| NAQuery on NADownload Ideal Coordinates CCD File | E [auth A]K [auth B]O [auth C]P [auth C]Q [auth C]E [auth A],K [auth B],O [auth C],P [auth C],Q [auth C],R [auth C],S [auth C] | SODIUM IONNaFKNQFGJONOIPTF-UHFFFAOYSA-N |  |
Interactions Interactions & Density |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.80 Å
- R-Value Free: 0.304 (Depositor), 0.300 (DCC)
- R-Value Work: 0.248 (Depositor), 0.250 (DCC)
- R-Value Observed: 0.251 (Depositor)
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 114.908 | α = 90 |
| b = 114.908 | β = 90 |
| c = 118.832 | γ = 90 |
Software Package:
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
Revision History (Full details and data files)
- Version 1.0: 2009-05-12
Type: Initial release - Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 1.2: 2019-02-27
Changes: Data collection, Database references - Version 1.3: 2021-10-20
Changes: Database references, Derived calculations - Version 1.4: 2023-08-30
Changes: Data collection, Refinement description - Version 1.5: 2024-11-13
Changes: Structure summary