MolNFT v1 · #105951 · protein
Wolinella succinogenes octaheme sulfite reductase mcca, form I
4RKM: “Wolinella succinogenes octaheme sulfite reductase mcca, form I”. X-ray diffraction, 4 ligands (HEM, SX, SO2), 20 pockets (best druggability 0.90). MolNFT v1 #105951 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4RKM
- Type
- protein
- Length
- 7,909 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mcca
- UniProt
- Q7MSJ8
- Ligands
- HEM, SX, SO2, CU1
- 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, C, D, E, F, I, J, K, L | Mcca | protein | 659 | 42% helix, 11% strand | Q7MSJ8 |
| B, H | Mcca | protein | 660 | 41% helix, 11% strand | Q7MSJ8 |
| G | Mcca | protein | 658 | 42% helix, 11% strand | Q7MSJ8 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 96 copies · chains A, B, C, F, D, K, E, H, I, J, L, G
- SX · Sulfur oxide · ligand · 10 copies · chains A, B, C, E, F, H, J, K, L, G
- SO2 · Sulfur dioxide · ligand · 4 copies · chains A, D, I, G
- CU1 · Copper (I) ion · metal · 12 copies · chains A, B, C, D, E, F, H, I, J, K, L, G
- BU3 · (R,R)-2,3-butanediol · additive · 27 copies · chains A, C, B, I, D, E, K, F, J, H, G, L
- ACT · Acetate ion · additive · 12 copies · chains A, B, C, D, E, F, H, I, J, K, L, G
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 | 1060 | 0.90 | 0.91 | 137 | CU1, SX, HEM |
| 2 | 1193 | 0.89 | 0.91 | 158 | CU1, SO2, HEM |
| 3 | 731 | 0.89 | 0.93 | 112 | HEM, CU1, SX |
| 4 | 684 | 0.89 | 0.93 | 95 | HEM, SX, SO2 |
| 5 | 706 | 0.89 | 0.93 | 111 | CU1, SX, HEM |
Interfaces
26 interfaces between chains.
- H–L · 2252 Ų buried · 36 hydrogen bonds · protein-protein
- L–G · 2227 Ų buried · 32 hydrogen bonds · protein-protein
- I–J · 2227 Ų buried · 35 hydrogen bonds · protein-protein
- D–K · 2223 Ų buried · 39 hydrogen bonds · protein-protein
- F–I · 2223 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 172 cofactor (heme attachment).
Compared structures
- 4RKM · Wolinella succinogenes octaheme sulfite reductase MccA, form I · the same entry in another collection · chain G against G, 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 Q7MSJ8
- Elsewhere: RCSB PDB 4RKM · PDBe 4RKM · UniProt Q7MSJ8
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