MolNFT v1 · #118292 · protein
Crystal structure of M. tuberculosis lipoyl synthase with 6- thiooctanoyl peptide intermediate
5EXK: “Crystal structure of M. tuberculosis lipoyl synthase with 6- thiooctanoyl peptide intermediate”. X-ray diffraction, 5 ligands (F3S, SF4, 5AD), 20 pockets (best druggability 0.86). MolNFT v1 #118292 on GenesisL1: 3D structure…
- PDB
- 5EXK
- Type
- protein
- Length
- 1,836 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipoyl synthase; Octanoylated peptide from M. tuberculosis H protein
- EC
- 2.8.1.8
- UniProt
- P9WK91
- Ligands
- F3S, SF4, 5AD, MET, CL
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 8 distinct chains · 41% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lipoyl synthase (EC 2.8.1.8) | protein | 306 | 42% helix, 14% strand | P9WK91 |
| B, D | Octanoylated peptide from M. tuberculosis H protein | protein | 8 | 0% helix, 0% strand | — |
| C | Lipoyl synthase (EC 2.8.1.8) | protein | 300 | 43% helix, 14% strand | P9WK91 |
| E | Lipoyl synthase (EC 2.8.1.8) | protein | 302 | 42% helix, 13% strand | P9WK91 |
| F, H, L | Octanoylated peptide from M. tuberculosis H protein | protein | 6 | 0% helix, 0% strand | — |
| G | Lipoyl synthase (EC 2.8.1.8) | protein | 296 | 42% helix, 15% strand | P9WK91 |
| I, K | Lipoyl synthase (EC 2.8.1.8) | protein | 296 | 40% helix, 15% strand | P9WK91 |
| J | Octanoylated peptide from M. tuberculosis H protein | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- F3S · FE3-S4 cluster · ligand · 6 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- SF4 · Iron/sulfur cluster · ligand · 6 copies · chains A, C, E, G, I, K
- 5AD · 5'-deoxyadenosine · ligand · 6 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- MET · Methionine · ligand · 6 copies · chains A, C, E, G, I, K
- CL · Chloride ion · ion · 2 copies · chains A, K
- IMD · Imidazole · additive · 2 copies · chains A, E
- IPA · Isopropyl alcohol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 274 | 0.86 | 0.98 | 36 | SF4, 5AD, MET |
| 2 | 274 | 0.86 | 0.97 | 34 | SF4, 5AD, MET |
| 3 | 283 | 0.86 | 0.96 | 35 | SF4, 5AD, MET |
| 4 | 304 | 0.85 | 0.96 | 41 | SF4, 5AD, MET, IMD |
| 5 | 261 | 0.85 | 0.97 | 36 | SF4, 5AD, MET |
Interfaces
14 interfaces between chains.
- A–K · 827 Ų buried · 13 hydrogen bonds · protein-protein
- C–G · 726 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 705 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 703 Ų buried · 11 hydrogen bonds · protein-protein
- G–H · 623 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (nonstandard).
Compared structures
- 5EXK · Crystal structure of M. tuberculosis lipoyl synthase with 6-thiooctanoyl peptide… · the same entry in another collection · chain L against L, 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 P9WK91
- Elsewhere: RCSB PDB 5EXK · PDBe 5EXK · UniProt P9WK91
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