Research workbench
Sliding helix induced change of coordination geometry in a model di-MN(II) protein
Analyse Sliding helix induced change of coordination geometry in a model di-MN(II)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LT1
- Type
- protein
- Length
- 384 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L13G-DF1
- Ligands
- ACE, MN, NH2
- Pockets
- 2 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 85% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | L13G-DF1 | protein | 48 | 85% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- MN · Manganese (II) ion · metal · 12 copies · chains A, B, H, C, D, E, F, G
- NH2 · Amino group · ion · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 558 | 0.66 | 0.77 | 34 | ACE, MN |
| 2 | 69 | 0.61 | 0.91 | 16 | empty |
Interfaces
14 interfaces between chains.
- E–F · 1025 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1014 Ų buried · 8 hydrogen bonds · protein-protein
- G–H · 927 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 887 Ų buried · 9 hydrogen bonds · protein-protein
- B–H · 241 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 1LT1 · Sliding helix induced change of coordination geometry in a model di-MN(II) protein · 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
- Elsewhere: RCSB PDB 1LT1 · PDBe 1LT1
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