MolNFT v1 · #104162 · protein
The crystal structure of an endo-1,4-D-glucanase from pseudomonas putida KT2440
4Q2B · Endo-1,4-beta-D-glucanase: “The crystal structure of an endo-1,4-D-glucanase from pseudomonas putida KT2440”. X-ray diffraction, 1 ligand (SO4), 17 pockets (best druggability 0.76). MolNFT v1 #104162 on GenesisL1: 3D structure…
- PDB
- 4Q2B
- Type
- protein
- Length
- 2,058 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-1,4-beta-D-glucanase
- UniProt
- Q88JL2
- Ligands
- SO4
- Pockets
- 17 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Endo-1,4-beta-D-glucanase | protein | 342 | 48% helix, 15% strand | Q88JL2 |
| B, D | Endo-1,4-beta-D-glucanase | protein | 344 | 49% helix, 14% strand | Q88JL2 |
| C, F | Endo-1,4-beta-D-glucanase | protein | 343 | 49% helix, 17% strand | Q88JL2 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, E, C, D, F
- FMT · Formic acid · additive · 9 copies · chains A, C, B, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains A, D, E, F
- GOL · Glycerol · additive · 3 copies · chains C, D
- MLA · Malonic acid · additive · chains C, D
- IMD · Imidazole · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 971 | 0.76 | 0.78 | 116 | IMD |
| 2 | 538 | 0.69 | 0.79 | 59 | SO4 |
| 3 | 459 | 0.59 | 0.75 | 72 | FMT |
| 4 | 295 | 0.57 | 0.77 | 51 | empty |
| 5 | 348 | 0.54 | 0.74 | 65 | empty |
Interfaces
6 interfaces between chains.
- E–F · 929 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 919 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 884 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 598 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 463 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 4Q2B · The crystal structure of an endo-1,4-D-glucanase from Pseudomonas putida KT2440 · the same entry in another collection · 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 Q88JL2
- Elsewhere: RCSB PDB 4Q2B · PDBe 4Q2B · UniProt Q88JL2
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