MolNFT v1 · #105952 · protein
Wolinella succinogenes octaheme sulfite reductase mcca, form II
4RKN: “Wolinella succinogenes octaheme sulfite reductase mcca, form II”. X-ray diffraction, 4 ligands (HEM, DTN, CU), 20 pockets (best druggability 0.90). MolNFT v1 #105952 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4RKN
- Type
- protein
- Length
- 2,639 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mcca
- UniProt
- Q7MSJ8
- Ligands
- HEM, DTN, CU, SO3
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mcca | protein | 660 | 42% helix, 11% strand | Q7MSJ8 |
| B, D | Mcca | protein | 660 | 43% helix, 11% strand | Q7MSJ8 |
| C | Mcca | protein | 659 | 42% helix, 11% strand | Q7MSJ8 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 32 copies · chains A, C, B, D
- DTN · Dithionite · ligand · 5 copies · chains A, B, C, D
- CU · Copper (II) ion · metal · 4 copies · chains A, B, C, D
- SO3 · Sulfite ion · ion · 5 copies · chains A, B, C, D
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 | 781 | 0.90 | 0.93 | 125 | HEM, CU, SO3 |
| 2 | 716 | 0.89 | 0.93 | 105 | HEM, CU, SO3 |
| 3 | 1174 | 0.88 | 0.90 | 133 | HEM, SO3 |
| 4 | 556 | 0.88 | 0.93 | 62 | HEM, SO3 |
| 5 | 166 | 0.78 | 0.94 | 48 | HEM |
Interfaces
4 interfaces between chains.
- B–C · 2239 Ų buried · 37 hydrogen bonds · protein-protein
- A–C · 2155 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 2093 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 374 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 59 cofactor (heme attachment).
Compared structures
- 4RKN · Wolinella succinogenes octaheme sulfite reductase MccA, form II · the same entry in another collection · chain B against B, TM-score 1.00
- Q7MSJ8 · AlphaFold monomer V2.0 prediction for dissimilatory sulfite reductase mcca (Q7MSJ8) · a predicted model of the same protein · chain C 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 Q7MSJ8
- Elsewhere: RCSB PDB 4RKN · PDBe 4RKN · UniProt Q7MSJ8
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