Research workbench
Crystal structure of lumazine synthase from salmonella typhimurium LT2
Analyse Crystal structure of lumazine synthase from salmonella typhimurium LT2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MK3
- Type
- protein
- Length
- 9,240 residues
- Chains
- 60
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6,7-dimethyl-8-ribityllumazine synthase
- EC
- 2.5.1.78
- UniProt
- P66038
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 24% 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, Y, Z, 1, 2, 3, 4, 5, 6, 7, 8, 9, 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 | 6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.78) | protein | 154 | 49% helix, 24% strand | P66038 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 79 copies · chains A, B, C, D, E, F, G, H, I, K, O, L, M, N, P, T, Q, R, S, U, Y, V, W, Z, 4, 1, 2, 3, 5, 9, 6, 7, X, 8, a, e, b, c, d, f, j, g, h, i, k, l, m, n, o, p, t, q, r, s, u, v, w, x, y, J
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 | 1104 | 0.87 | 0.89 | 98 | SO4 |
| 2 | 1053 | 0.87 | 0.88 | 96 | SO4 |
| 3 | 1097 | 0.87 | 0.88 | 99 | SO4 |
| 4 | 1055 | 0.87 | 0.88 | 99 | SO4 |
| 5 | 1134 | 0.87 | 0.88 | 95 | SO4 |
Interfaces
150 interfaces between chains.
- g–h · 1408 Ų buried · 17 hydrogen bonds · protein-protein
- k–l · 1394 Ų buried · 17 hydrogen bonds · protein-protein
- v–w · 1393 Ų buried · 15 hydrogen bonds · protein-protein
- 5–9 · 1393 Ų buried · 17 hydrogen bonds · protein-protein
- s–t · 1390 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3MK3 · Crystal structure of Lumazine synthase from Salmonella typhimurium LT2 · 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 P66038
- Elsewhere: RCSB PDB 3MK3 · PDBe 3MK3 · UniProt P66038
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