Research workbench
The archaellum of methanocaldococcus villosus
Analyse The archaellum of methanocaldococcus villosus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OFQ
- Type
- protein
- Length
- 9,493 residues
- Chains
- 45
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Archaellin
- Ligands
- UNL, CA
- Pockets
- 20 · best druggability 0.90
Structure
electron microscopy · 2 distinct chains · 27% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K, M, O, Q, S, U, W, Y, a, c, e, g, i, k, m, o, q, s | Archaellin | protein | 209 | 27% helix, 34% strand | — |
| B, D, F, H, J, L, N, P, R, T, V, X, Z, b, d, f, h, j, l, n, p, r | Archaellin | protein | 213 | 27% helix, 40% strand | — |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 804 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, Y, Z, a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s
- CA · Calcium ion · metal · 45 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, Y, Z, a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s
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 | 1058 | 0.90 | 0.93 | 181 | empty |
| 2 | 1018 | 0.90 | 0.92 | 174 | empty |
| 3 | 979 | 0.90 | 0.92 | 164 | empty |
| 4 | 889 | 0.90 | 0.93 | 147 | empty |
| 5 | 583 | 0.87 | 0.93 | 101 | empty |
Interfaces
243 interfaces between chains.
- f–g · 1791 Ų buried · 11 hydrogen bonds · protein-protein
- h–i · 1777 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 1771 Ų buried · 12 hydrogen bonds · protein-protein
- N–O · 1771 Ų buried · 10 hydrogen bonds · protein-protein
- R–S · 1768 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 201 covalent (covalent ligand).
Compared structures
- 7OFQ · The archaellum of Methanocaldococcus villosus · 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 7OFQ · PDBe 7OFQ
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