Research workbench
Silver-bound glyceraldehyde-3-phosphate dehydrogenase a
Analyse Silver-bound glyceraldehyde-3-phosphate dehydrogenase a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IO4
- Type
- protein
- Length
- 5,264 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyceraldehyde-3-phosphate dehydrogenase a
- EC
- 1.2.1.12
- UniProt
- P0A9B2
- Ligands
- AG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P | Glyceraldehyde-3-phosphate dehydrogenase a (EC 1.2.1.12) | protein | 329 | 28% helix, 28% strand | P0A9B2 |
Ligands and binding sites
- AG · Silver ion · metal · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
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 | 820 | 0.82 | 0.85 | 111 | empty |
| 2 | 913 | 0.82 | 0.84 | 124 | empty |
| 3 | 1125 | 0.79 | 0.81 | 125 | empty |
| 4 | 815 | 0.76 | 0.80 | 82 | empty |
| 5 | 1009 | 0.76 | 0.79 | 117 | empty |
Interfaces
35 interfaces between chains.
- M–N · 2051 Ų buried · 28 hydrogen bonds · protein-protein
- G–H · 2051 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 2046 Ų buried · 28 hydrogen bonds · protein-protein
- K–L · 2045 Ų buried · 27 hydrogen bonds · protein-protein
- I–J · 2045 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 6IO4 · Silver-bound Glyceraldehyde-3-phosphate dehydrogenase A · the same entry in another collection · chain J against J, 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 P0A9B2
- Elsewhere: RCSB PDB 6IO4 · PDBe 6IO4 · UniProt P0A9B2
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