Research workbench
Avian respiratory complex II with carboxin bound
Analyse Avian respiratory complex II with carboxin bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FBW
- Type
- protein
- Length
- 2,185 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial; Succinate…
- EC
- 1.3.5.1
- UniProt
- F1NPJ4, Q9YHT2, A0A3Q2U2Y6, Q5ZIS0
- Ligands
- UNL, FAD, Y3P, FES, SF4, F3S, HEM, CBE, UMQ, K, NA, AZI
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 5 distinct chains · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, N | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial (EC 1.3.5.1) | protein | 612 | 35% helix, 21% strand | F1NPJ4 |
| B | Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial (EC 1.3.5.1) | protein | 240 | 32% helix, 15% strand | Q9YHT2 |
| C, P | Succinate dehydrogenase cytochrome B560 subunit, mitochondrial | protein | 139 | 76% helix, 1% strand | A0A3Q2U2Y6 |
| D, Q | Succinate dehydrogenase [ubiquinone] cytochrome B small subunit, mitochondrial | protein | 101 | 86% helix, 0% strand | Q5ZIS0 |
| O | Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial (EC 1.3.5.1) | protein | 241 | 32% helix, 15% strand | Q9YHT2 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 256 copies · chains A, B, C, D, P, O, N, Q
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B, N, O
- Y3P · (~{Z})-2-oxidanylbut-2-enedioic acid · ligand · 2 copies · chains A, N
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains B, O
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains B, O
- F3S · FE3-S4 cluster · ligand · 2 copies · chains B, O
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains B, C, D, O, P, Q
- CBE · 2-methyl-N-phenyl-5,6-dihydro-1,4-oxathiine-3-carboxamide · ligand · 2 copies · chains B, C, D, O, P, Q
- UMQ · Undecyl-maltoside · ligand · chains C, O, P
- K · Potassium ion · metal · 2 copies · chains A, N
- NA · Sodium ion · metal · chains B
- AZI · Azide ion · ion · 3 copies · chains A, B, D, N
- BOG · octyl beta-D-glucopyranoside · additive · 3 copies · chains B, C, P, D
- GOL · Glycerol · additive · 2 copies · chains B, C, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 324 | 0.86 | 0.96 | 56 | FAD, Y3P |
| 2 | 314 | 0.85 | 0.96 | 55 | FAD, Y3P |
| 3 | 1057 | 0.85 | 0.86 | 93 | UNL, HEM, CBE |
| 4 | 1185 | 0.83 | 0.84 | 99 | AZI, UNL, HEM, CBE |
| 5 | 489 | 0.78 | 0.85 | 50 | UNL |
Interfaces
15 interfaces between chains.
- A–B · 2678 Ų buried · 50 hydrogen bonds · protein-protein
- N–O · 2675 Ų buried · 47 hydrogen bonds · protein-protein
- O–P · 1807 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1804 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1380 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (flavinylation).
Compared structures
- 2FBW · Avian respiratory complex II with carboxin bound · the same entry in another collection · chain Q against Q, TM-score 1.00
- Q9YHT2 · AlphaFold monomer V2.0 prediction for succinate dehydrogenase [ubiquinone] iron-sulfur… · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q5ZIS0 · AlphaFold monomer V2.0 prediction for succinate dehydrogenase [ubiquinone] cytochrome B… · a predicted model of the same protein · chain D against A, TM-score 0.99
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 F1NPJ4
- Every structure of UniProt Q9YHT2
- Every structure of UniProt A0A3Q2U2Y6
- Every structure of UniProt Q5ZIS0
- Elsewhere: RCSB PDB 2FBW · PDBe 2FBW · UniProt F1NPJ4 · UniProt Q9YHT2 · UniProt A0A3Q2U2Y6 · UniProt Q5ZIS0
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