Research workbench
Xiaf from streptomyces sp. in complex with FADH2 and glycerol
Analyse Xiaf from streptomyces sp. in complex with FADH2 and glycerol in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MR6
- Type
- protein
- Length
- 9,504 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xiaf protein
- UniProt
- I7IIA9
- Ligands
- FAD
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 60% helix, 16% 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, Q, R, S, T, U, V, W, X | Xiaf protein | protein | 396 | 60% helix, 16% strand | I7IIA9 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 24 copies · chains A, D, B, C, E, H, F, G, I, L, J, K, M, P, N, O, Q, T, R, S, U, X, V, W
- GOL · Glycerol · additive · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, 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 | 933 | 0.87 | 0.88 | 123 | empty |
| 2 | 713 | 0.87 | 0.90 | 129 | empty |
| 3 | 667 | 0.86 | 0.90 | 130 | empty |
| 4 | 1149 | 0.86 | 0.87 | 115 | empty |
| 5 | 1182 | 0.86 | 0.87 | 115 | empty |
Interfaces
44 interfaces between chains.
- Q–T · 2088 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 2085 Ų buried · 24 hydrogen bonds · protein-protein
- I–L · 2083 Ų buried · 24 hydrogen bonds · protein-protein
- E–H · 2081 Ų buried · 24 hydrogen bonds · protein-protein
- U–X · 2081 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 5MR6 · XiaF from Streptomyces sp. in complex with FADH2 and Glycerol · 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 I7IIA9
- Elsewhere: RCSB PDB 5MR6 · PDBe 5MR6 · UniProt I7IIA9
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