MolNFT v1 · #169023 · protein
Crystal structure of chlamydia trachomatis glyceraldehyde 3-phosphate dehydrogenase
6WYC · Glyceraldehyde-3-phosphate dehydrogenase: “Crystal structure of chlamydia trachomatis glyceraldehyde 3-phosphate dehydrogenase”. X-ray diffraction, 1 ligand (NAD), 8 pockets (best druggability 0.81). MolNFT v1 #169023 on GenesisL1…
- PDB
- 6WYC
- Type
- protein
- Length
- 1,329 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
- 8 · best druggability 0.81
Structure
x-ray diffraction · 3 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 | 333 | 30% helix, 26% strand | P0CE13 |
| B, C | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) | protein | 332 | 30% helix, 27% strand | P0CE13 |
| D | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) | protein | 332 | 29% helix, 27% strand | P0CE13 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 994 | 0.81 | 0.82 | 122 | empty |
| 2 | 494 | 0.72 | 0.81 | 66 | NAD |
| 3 | 435 | 0.71 | 0.82 | 61 | NAD |
| 4 | 410 | 0.70 | 0.82 | 55 | NAD |
| 5 | 452 | 0.70 | 0.81 | 51 | NAD |
Interfaces
6 interfaces between chains.
- A–B · 1950 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 1950 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 1513 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1482 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 467 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (artifact, nonstandard).
Compared structures
- 6WYC · Crystal Structure of Chlamydia trachomatis Glyceraldehyde 3-phosphate dehydrogenase · 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 6WYC · PDBe 6WYC · UniProt P0CE13
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