Research workbench
Crystal structure of transaldolase (ec 2.2.1.2) (TM0295) from thermotoga maritima at 2.40 a resolution
Analyse Crystal structure of transaldolase (ec 2.2.1.2) (TM0295) from thermotoga… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VPX
- Type
- protein
- Length
- 4,176 residues
- Chains
- 20
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (transaldolase (ec 2.2.1.2))
- EC
- 2.2.1.2
- UniProt
- Q9WYD1
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · 17 distinct chains · 52% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (transaldolase (ec 2.2.1.2)) (EC 2.2.1.2) | protein | 207 | 53% helix, 18% strand | Q9WYD1 |
| B, P | Protein (transaldolase (ec 2.2.1.2)) (EC 2.2.1.2) | protein | 209 | 52% helix, 18% strand | Q9WYD1 |
| C | Protein (transaldolase (ec 2.2.1.2)) (EC 2.2.1.2) | protein | 208 | 52% helix, 18% strand | Q9WYD1 |
| D, O | Protein (transaldolase (ec 2.2.1.2)) (EC 2.2.1.2) | protein | 210 | 52% helix, 18% strand | Q9WYD1 |
| E, K | Protein (transaldolase (ec 2.2.1.2)) (EC 2.2.1.2) | protein | 216 | 55% helix, 18% strand | Q9WYD1 |
| F | Protein (transaldolase (ec 2.2.1.2)) (EC 2.2.1.2) | protein | 213 | 52% helix, 18% strand | Q9WYD1 |
| G | Protein (transaldolase (ec 2.2.1.2)) (EC 2.2.1.2) | protein | 216 | 53% helix, 18% strand | Q9WYD1 |
| H | Protein (transaldolase (ec 2.2.1.2)) (EC 2.2.1.2) | protein | 205 | 52% helix, 19% strand | Q9WYD1 |
| I | Protein (transaldolase (ec 2.2.1.2)) (EC 2.2.1.2) | protein | 211 | 52% helix, 18% strand | Q9WYD1 |
| J | Protein (transaldolase (ec 2.2.1.2)) (EC 2.2.1.2) | protein | 213 | 54% helix, 18% strand | Q9WYD1 |
| L | Protein (transaldolase (ec 2.2.1.2)) (EC 2.2.1.2) | protein | 204 | 51% helix, 19% strand | Q9WYD1 |
| M | Protein (transaldolase (ec 2.2.1.2)) (EC 2.2.1.2) | protein | 198 | 52% helix, 19% strand | Q9WYD1 |
| N | Protein (transaldolase (ec 2.2.1.2)) (EC 2.2.1.2) | protein | 204 | 53% helix, 19% strand | Q9WYD1 |
| Q | Protein (transaldolase (ec 2.2.1.2)) (EC 2.2.1.2) | protein | 208 | 53% helix, 18% strand | Q9WYD1 |
| R | Protein (transaldolase (ec 2.2.1.2)) (EC 2.2.1.2) | protein | 210 | 52% helix, 18% strand | Q9WYD1 |
| S | Protein (transaldolase (ec 2.2.1.2)) (EC 2.2.1.2) | protein | 205 | 52% helix, 19% strand | Q9WYD1 |
| T | Protein (transaldolase (ec 2.2.1.2)) (EC 2.2.1.2) | protein | 204 | 51% helix, 19% strand | Q9WYD1 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains O
- GOL · Glycerol · additive · 21 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 406 | 0.68 | 0.80 | 51 | empty |
| 2 | 360 | 0.66 | 0.80 | 53 | empty |
| 3 | 238 | 0.66 | 0.83 | 26 | empty |
| 4 | 322 | 0.65 | 0.80 | 35 | empty |
| 5 | 274 | 0.63 | 0.80 | 36 | empty |
Interfaces
54 interfaces between chains.
- A–E · 1743 Ų buried · 17 hydrogen bonds · protein-protein
- K–O · 1719 Ų buried · 18 hydrogen bonds · protein-protein
- F–G · 1715 Ų buried · 17 hydrogen bonds · protein-protein
- P–Q · 1705 Ų buried · 16 hydrogen bonds · protein-protein
- F–J · 1685 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 1VPX · Crystal structure of Transaldolase (EC 2.2.1.2) (TM0295) from Thermotoga maritima at 2.40… · the same entry in another collection · chain H against H, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9WYD1
- Elsewhere: RCSB PDB 1VPX · PDBe 1VPX · UniProt Q9WYD1
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