Research workbench
Crystal structure of the N. meningitides methionine-binding protein in its D-methionine bound conformation.
Analyse Crystal structure of the N. meningitides methionine-binding protein in its… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DZX
- Type
- protein
- Length
- 1,445 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipoprotein
- UniProt
- C6S9R8
- Ligands
- MED
- Pockets
- 16 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Lipoprotein | protein | 240 | 40% helix, 23% strand | C6S9R8 |
| B, C, D | Lipoprotein | protein | 241 | 40% helix, 24% strand | C6S9R8 |
| E | Lipoprotein | protein | 242 | 40% helix, 24% strand | C6S9R8 |
Ligands and binding sites
- MED · D-methionine · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 851 | 0.80 | 0.82 | 91 | empty |
| 2 | 883 | 0.78 | 0.81 | 80 | empty |
| 3 | 509 | 0.73 | 0.82 | 61 | empty |
| 4 | 54 | 0.72 | 0.99 | 22 | MED |
| 5 | 52 | 0.72 | 0.99 | 18 | MED |
Interfaces
9 interfaces between chains.
- B–E · 755 Ų buried · 10 hydrogen bonds · protein-protein
- D–F · 732 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 704 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 691 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 583 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6DZX · Crystal structure of the N. meningitides methionine-binding protein in its D-methionine… · 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 C6S9R8
- Elsewhere: RCSB PDB 6DZX · PDBe 6DZX · UniProt C6S9R8
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