Research workbench
Crystal structure of METHANOL:COBALAMIN methyltransferase complex mtabc from methanosarcina barkeri
Analyse Crystal structure of METHANOL:COBALAMIN methyltransferase complex mtabc from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2I2X
- Type
- protein
- Length
- 5,736 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyltransferase 1
- EC
- 2.1.1.90
- UniProt
- P94921, P94920
- Ligands
- B13, ZN, K
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K, M, O | Methyltransferase 1 (EC 2.1.1.90) | protein | 459 | 56% helix, 12% strand | P94921 |
| B, D, F, H, J, L, N, P | Methyltransferase 1 (EC 2.1.1.90) | protein | 258 | 52% helix, 10% strand | P94920 |
Ligands and binding sites
- B13 · 5-hydroxybenzimidazolylcob(iii)amide · ligand · 8 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
- ZN · Zinc ion · metal · 12 copies · chains A, C, E, G, I, K, M, O
- K · Potassium ion · metal · 8 copies · chains A, C, E, G, I, K, M, O
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 | 982 | 0.84 | 0.85 | 113 | empty |
| 2 | 1017 | 0.83 | 0.84 | 100 | K, B13 |
| 3 | 1142 | 0.83 | 0.84 | 116 | K, B13 |
| 4 | 1031 | 0.83 | 0.84 | 96 | K, B13 |
| 5 | 1062 | 0.83 | 0.84 | 105 | K, B13 |
Interfaces
32 interfaces between chains.
- M–O · 2134 Ų buried · 43 hydrogen bonds · protein-protein
- I–K · 2130 Ų buried · 42 hydrogen bonds · protein-protein
- A–C · 2128 Ų buried · 42 hydrogen bonds · protein-protein
- E–G · 2108 Ų buried · 40 hydrogen bonds · protein-protein
- M–N · 2004 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 2I2X · Crystal structure of methanol:cobalamin methyltransferase complex MtaBC from… · the same entry in another collection · chain A against A, 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 P94921
- Every structure of UniProt P94920
- Elsewhere: RCSB PDB 2I2X · PDBe 2I2X · UniProt P94921 · UniProt P94920
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