MolNFT v1 · #125590 · protein
Maltose binding protein genetically fused to dodecameric glutamine synthetase
5LDF: “Maltose binding protein genetically fused to dodecameric glutamine synthetase”. Electron microscopy, 1 ligand (GLC), 20 pockets (best druggability 0.81). MolNFT v1 #125590 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5LDF
- Type
- protein
- Length
- 10,032 residues
- Chains
- 24
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamine synthetase; Maltose-binding periplasmic protein
- EC
- 6.3.1.2
- UniProt
- P0A1P7, P0AEY0
- Ligands
- GLC
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 2 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Glutamine synthetase (EC 6.3.1.2) | protein | 466 | 36% helix, 23% strand | P0A1P7 |
| M, N, O, P, Q, R, S, T, U, V, W, X | Maltose-binding periplasmic protein | protein | 370 | 44% helix, 21% strand | P0AEY0 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 24 copies · chains M, N, O, P, Q, R, S, T, U, V, W, X
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 | 954 | 0.81 | 0.83 | 88 | empty |
| 2 | 949 | 0.81 | 0.83 | 95 | empty |
| 3 | 988 | 0.81 | 0.82 | 91 | empty |
| 4 | 966 | 0.81 | 0.82 | 88 | empty |
| 5 | 873 | 0.80 | 0.83 | 80 | empty |
Interfaces
36 interfaces between chains.
- B–H · 2844 Ų buried · 32 hydrogen bonds · protein-protein
- A–G · 2842 Ų buried · 33 hydrogen bonds · protein-protein
- C–I · 2841 Ų buried · 32 hydrogen bonds · protein-protein
- F–L · 2841 Ų buried · 32 hydrogen bonds · protein-protein
- D–J · 2836 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 5LDF · Maltose binding protein genetically fused to dodecameric glutamine synthetase · 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 P0A1P7
- Every structure of UniProt P0AEY0
- Elsewhere: RCSB PDB 5LDF · PDBe 5LDF · UniProt P0A1P7 · UniProt P0AEY0
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