Research workbench
Crystal structure of anapt from neosartorya fischeri
Analyse Crystal structure of anapt from neosartorya fischeri in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LD7
- Type
- protein
- Length
- 6,341 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dimethylallyl tryptophan synthase
- EC
- 2.5.1.34
- UniProt
- A1DN10
- Ligands
- PIS, NA
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, L, M, N, P | Dimethylallyl tryptophan synthase (EC 2.5.1.34) | protein | 397 | 42% helix, 20% strand | A1DN10 |
| K | Dimethylallyl tryptophan synthase (EC 2.5.1.34) | protein | 392 | 42% helix, 20% strand | A1DN10 |
| O | Dimethylallyl tryptophan synthase (EC 2.5.1.34) | protein | 391 | 42% helix, 20% strand | A1DN10 |
Ligands and binding sites
- PIS · Trihydrogen thiodiphosphate · ligand · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
- NA · Sodium 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 | 261 | 0.82 | 0.94 | 56 | empty |
| 2 | 232 | 0.82 | 0.95 | 54 | empty |
| 3 | 235 | 0.81 | 0.94 | 57 | empty |
| 4 | 250 | 0.81 | 0.94 | 50 | empty |
| 5 | 888 | 0.80 | 0.82 | 120 | empty |
Interfaces
32 interfaces between chains.
- A–B · 1054 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 1033 Ų buried · 4 hydrogen bonds · protein-protein
- G–H · 1029 Ų buried · 3 hydrogen bonds · protein-protein
- M–N · 1023 Ų buried · 2 hydrogen bonds · protein-protein
- K–L · 1005 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4LD7 · Crystal structure of AnaPT from Neosartorya fischeri · 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 A1DN10
- Elsewhere: RCSB PDB 4LD7 · PDBe 4LD7 · UniProt A1DN10
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