Research workbench
Structure of a N-me-P-iodo-D-PHE1,N-me-D-GLN4,LYS10-teixobactin analogue
Analyse Structure of a N-me-P-iodo-D-PHE1,N-me-D-GLN4,LYS10-teixobactin analogue in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6E00
- Type
- protein
- Length
- 352 residues
- Chains
- 32
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-me-P-iodo-D-PHE1,N-me-D-GLN4,LYS10-teixobactin analogue
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.92
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p | N-me-P-iodo-D-PHE1,N-me-D-GLN4,LYS10-teixobactin analogue | protein | 11 | 0% helix, 45% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 32 copies · chains A, B, C, c, D, E, F, G, k, H, I, J, K, f, L, M, p, N, O, P, a, b, d, e, g, h, i, j, l, m, n, o
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1121 | 0.92 | 0.92 | 84 | empty |
| 2 | 76 | 0.38 | 0.77 | 18 | SO4 |
| 3 | 90 | 0.38 | 0.76 | 19 | SO4 |
Interfaces
163 interfaces between chains.
- o–p · 449 Ų buried · 9 hydrogen bonds · protein-protein
- O–P · 442 Ų buried · 10 hydrogen bonds · protein-protein
- m–n · 436 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 432 Ų buried · 9 hydrogen bonds · protein-protein
- b–c · 429 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 96 modified, 32 d-amino (nonstandard, D-amino acid).
Compared structures
- 6E00 · Structure of a N-Me-p-iodo-D-Phe1,N-Me-D-Gln4,Lys10-teixobactin analogue · the same entry in another collection · chain B against B, 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 6E00 · PDBe 6E00
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