MolNFT v1 · #169154 · protein
Crystal structure of chlamydia trachomatis mixed (APO/HOLO) glyceraldehyde 3-phosphate dehydrogenase
6X2E · Glyceraldehyde-3-phosphate dehydrogenase: “Crystal structure of chlamydia trachomatis mixed (APO/HOLO) glyceraldehyde 3-phosphate dehydrogenase”. X-ray diffraction, 1 ligand (NAD), 9 pockets (best druggability 0.81). MolNFT v1…
- PDB
- 6X2E
- Type
- protein
- Length
- 1,328 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyceraldehyde-3-phosphate dehydrogenase
- EC
- 1.2.1.12
- UniProt
- P0CE13
- Ligands
- NAD
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) | protein | 332 | 31% helix, 26% strand | P0CE13 |
| B | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) | protein | 332 | 30% helix, 26% strand | P0CE13 |
| C | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) | protein | 333 | 31% helix, 26% strand | P0CE13 |
| D | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) | protein | 331 | 29% helix, 26% strand | P0CE13 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 3 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 890 | 0.81 | 0.83 | 109 | empty |
| 2 | 485 | 0.72 | 0.81 | 64 | NAD |
| 3 | 474 | 0.72 | 0.82 | 58 | NAD |
| 4 | 590 | 0.71 | 0.79 | 57 | NAD |
| 5 | 546 | 0.69 | 0.79 | 63 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1941 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1930 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 1508 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1506 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 460 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (artifact, nonstandard).
Compared structures
- 6X2E · Crystal Structure of Chlamydia trachomatis mixed (apo/holo) Glyceraldehyde 3-phosphate… · the same entry in another collection · chain D against D, TM-score 1.00
- P0CE13 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase (P0CE13) · a predicted model of the same protein · chain A against A, 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 P0CE13
- Elsewhere: RCSB PDB 6X2E · PDBe 6X2E · UniProt P0CE13
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