Download MendeleyCrystal structure of glycerol-3-phosphate dehydrogenase (TM0378) from Thermotoga maritima at 2.00 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
1Z82
Crystal structure of glycerol-3-phosphate dehydrogenase (TM0378) from THERMOTOGA MARITIMA at 2.00 A resolution
- PDB DOI: https://doi.org/10.2210/pdb1Z82/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Thermotoga maritima MSB8
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2005-03-29 Released: 2005-04-12
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.211
- R-Value Work: 0.166
- R-Value Observed: 0.168
This is version 1.4 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 |
| glycerol-3-phosphate dehydrogenase | 335 | Thermotoga maritima MSB8 | Mutation(s): 11 Gene Names: TM0378 EC: 1.1.1.8 (PDB Primary Data), 1.1.1.94 (UniProt) |  | |
UniProt | |||||
Find proteins for A0A0F6AK91 (Thermotoga sp. (strain RQ2)) Explore A0A0F6AK91 Go to UniProtKB: A0A0F6AK91 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A0A0F6AK91 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 5 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NDP Query on NDP | C [auth A], I [auth B] | NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N |  | ||
| G3P Query on G3P | J [auth B] | SN-GLYCEROL-3-PHOSPHATE C3 H9 O6 P AWUCVROLDVIAJX-GSVOUGTGSA-N |  | ||
| G3H Query on G3H | D [auth A] | GLYCERALDEHYDE-3-PHOSPHATE C3 H7 O6 P LXJXRIRHZLFYRP-VKHMYHEASA-N |  | ||
| MPD Query on MPD | F [auth A], G [auth A], H [auth A] | (4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N |  | ||
| MRD Query on MRD | E [auth A], K [auth B], L [auth B], M [auth B], N [auth B] | (4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A, B | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.211
- R-Value Work: 0.166
- R-Value Observed: 0.168
- Space Group: P 1 21 1
- Diffraction Data: https://doi.org/10.18430/M31Z82
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 65.09 | α = 90 |
| b = 67.451 | β = 113.67 |
| c = 75.597 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| SCALA | data scaling |
| PDB_EXTRACT | data extraction |
| MOSFLM | data reduction |
| CCP4 | data scaling |
| SOLVE | phasing |
Entry History
Deposition Data
- Released Date: 2005-04-12 Deposition Author(s): Joint Center for Structural Genomics (JCSG)
Revision History (Full details and data files)
- Version 1.0: 2005-04-12
Type: Initial release - Version 1.1: 2008-04-30
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance - Version 1.3: 2023-01-25
Changes: Database references, Derived calculations - Version 1.4: 2024-10-30
Changes: Data collection, Refinement description, Structure summary
