MolNFT v1 · #78530 · protein
Structure of E.COLI gdh from native source
3SBO · NADP-specific glutamate dehydrogenase: “Structure of E.COLI gdh from native source”. X-ray diffraction, 1 ligand (CL), 20 pockets (best druggability 0.83). MolNFT v1 #78530 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3SBO
- Type
- protein
- Length
- 2,636 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADP-specific glutamate dehydrogenase
- EC
- 1.4.1.4
- UniProt
- P00370
- Ligands
- CL
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NADP-specific glutamate dehydrogenase (EC 1.4.1.4) | protein | 440 | 49% helix, 16% strand | P00370 |
| B | NADP-specific glutamate dehydrogenase (EC 1.4.1.4) | protein | 440 | 49% helix, 15% strand | P00370 |
| C, D | NADP-specific glutamate dehydrogenase (EC 1.4.1.4) | protein | 442 | 47% helix, 16% strand | P00370 |
| E | NADP-specific glutamate dehydrogenase (EC 1.4.1.4) | protein | 441 | 48% helix, 15% strand | P00370 |
| F | NADP-specific glutamate dehydrogenase (EC 1.4.1.4) | protein | 431 | 49% helix, 15% strand | P00370 |
Ligands and binding sites
- CL · Chloride ion · ion · 8 copies · chains A, C, D, E, F
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 | 987 | 0.83 | 0.84 | 122 | CL |
| 2 | 952 | 0.83 | 0.84 | 128 | empty |
| 3 | 914 | 0.79 | 0.81 | 81 | CL |
| 4 | 889 | 0.78 | 0.81 | 86 | empty |
| 5 | 403 | 0.78 | 0.87 | 45 | empty |
Interfaces
12 interfaces between chains.
- E–F · 1652 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 1595 Ų buried · 36 hydrogen bonds · protein-protein
- B–D · 1588 Ų buried · 39 hydrogen bonds · protein-protein
- A–D · 1092 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 1071 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
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 P00370
- Elsewhere: RCSB PDB 3SBO · PDBe 3SBO · UniProt P00370
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