Download MendeleyCrystal Structure of Metallo-beta-Lactamase SMB-1 Bound to Hydrolyzed Doripenem
Wachino, J., Arakawa, Y.To be published.
5B15
Crystal Structure of Metallo-beta-Lactamase SMB-1 Bound to Hydrolyzed Doripenem
- PDB DOI: https://doi.org/10.2210/pdb5B15/pdb
- Classification: HYDROLASE
- Organism(s): Serratia marcescens
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2015-11-23 Released: 2016-05-11
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.39 ?
- R-Value Free: 0.158
- R-Value Work: 0.136
- R-Value Observed: 0.138
Starting Model: experimental
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This is version 1.3 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Metallo-beta-lactamase | 262 | Serratia marcescens | Mutation(s): 0 Gene Names: SMB-1 EC: 3.5.2.6 |  | |
UniProt | |||||
Find proteins for G5ELM3 (Serratia marcescens) Explore G5ELM3 Go to UniProtKB: G5ELM3 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | G5ELM3 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| DQM Query on DQM | N [auth A] | (2~{S},3~{R},4~{S})-2-[(2~{S},3~{R})-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-3-methyl-4-[(3~{S},5~{S})-5-[(sulfamoylamino)methyl]pyrrolidin-3-yl]sulfanyl-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid C15 H26 N4 O7 S2 FODJFDYENOTZNC-UNWFBNKDSA-N |  | ||
| SO4 Query on SO4 | K [auth A], L [auth A], M [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| ZN Query on ZN | B [auth A], C [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| NA Query on NA | D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.39 ?
- R-Value Free: 0.158
- R-Value Work: 0.136
- R-Value Observed: 0.138
- Space Group: P 1
Unit Cell:
| Length ( ? ) | Angle ( ? ) |
|---|---|
| a = 37.01 | α = 107.57 |
| b = 40.92 | β = 102.56 |
| c = 45.32 | γ = 107.01 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| MOSFLM | data reduction |
| SCALA | data scaling |
| MOLREP | phasing |
Entry History
Deposition Data
- Released Date: 2016-05-11 Deposition Author(s): Wachino, J., Arakawa, Y.
Revision History (Full details and data files)
- Version 1.0: 2016-05-11
Type: Initial release - Version 1.1: 2016-07-06
Changes: Data collection - Version 1.2: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description - Version 1.3: 2024-10-23
Changes: Structure summary
