MolNFT v1 · #156142 · protein
Structure of mycobacterium smegmatis succinate dehydrogenase 2
6LUM: “Structure of mycobacterium smegmatis succinate dehydrogenase 2”. Electron microscopy, 10 ligands (PEV, HEM, MQ9). MolNFT v1 #156142 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6LUM
- Type
- protein
- Length
- 3,178 residues
- Chains
- 15
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Ligands
- PEV, HEM, MQ9, CDL, LPP, PIE, FAD, FES, SF4, F3S
Structure
electron microscopy · 11 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | — | protein | 122 | — | — |
| D | — | protein | 146 | — | — |
| E, I, O | — | protein | 31 | — | — |
| A, P | — | protein | 539 | — | — |
| B, Q | — | protein | 238 | — | — |
| G | — | protein | 123 | — | — |
| H | — | protein | 120 | — | — |
| J | — | protein | 534 | — | — |
| K | — | protein | 247 | — | — |
| M | — | protein | 123 | — | — |
| N | — | protein | 116 | — | — |
Ligands and binding sites
- PEV · (1S)-2-{[(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl stearate · ligand · 6 copies · chains C, D, B, E, G, I, K, M, O, H, Q
- HEM · Protoporphyrin IX containing Fe · ligand · 6 copies · chains C, D, B, G, H, K, M, N, Q
- MQ9 · Menaquinone-9 · ligand · 6 copies · chains D, H, N
- CDL · Cardiolipin · ligand · 3 copies · chains C, D, E, H, G, I, M, N, O
- LPP · 2-(hexadecanoyloxy)-1-[(phosphonooxy)methyl]ethyl hexadecanoate · ligand · 3 copies · chains D, M, O, C, H, G, I, N
- PIE · 1,2-diacyl-sn-glycero-3-phosphoinositol · ligand · 3 copies · chains D, E, G, H, I, M, N, O
- FAD · Flavin-adenine dinucleotide · ligand · 3 copies · chains A, J, P
- FES · Fe2/s2 (inorganic) cluster · ligand · 3 copies · chains B, K, Q
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains B, K, Q
- F3S · FE3-S4 cluster · ligand · 3 copies · chains B, K, Q
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Compared structures
- 6LUM · Structure of Mycobacterium smegmatis succinate dehydrogenase 2 · the same entry in another collection · chain C against C, 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 6LUM · PDBe 6LUM
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