Research workbench
Crystal structure of methenyltetrahydromethanopterin cyclohydrolase from methanobrevibacter ruminantium
Analyse Crystal structure of methenyltetrahydromethanopterin cyclohydrolase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FIO
- Type
- protein
- Length
- 960 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methenyltetrahydromethanopterin cyclohydrolase
- EC
- 3.5.4.27
- UniProt
- D3E4S5
- Ligands
- EEE
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methenyltetrahydromethanopterin cyclohydrolase (EC 3.5.4.27) | protein | 321 | 40% helix, 21% strand | D3E4S5 |
| B | Methenyltetrahydromethanopterin cyclohydrolase (EC 3.5.4.27) | protein | 320 | 41% helix, 21% strand | D3E4S5 |
| C | Methenyltetrahydromethanopterin cyclohydrolase (EC 3.5.4.27) | protein | 319 | 41% helix, 21% strand | D3E4S5 |
Ligands and binding sites
- EEE · Ethyl acetate · ligand · 2 copies · chains A, B
- IPA · Isopropyl alcohol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 638 | 0.74 | 0.80 | 76 | empty |
| 2 | 445 | 0.67 | 0.79 | 36 | EEE, IPA |
| 3 | 360 | 0.66 | 0.80 | 35 | empty |
| 4 | 286 | 0.63 | 0.80 | 26 | EEE, IPA |
| 5 | 161 | 0.52 | 0.79 | 21 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1440 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1415 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1365 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4FIO · Crystal Structure of Methenyltetrahydromethanopterin Cyclohydrolase 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 D3E4S5
- Elsewhere: RCSB PDB 4FIO · PDBe 4FIO · UniProt D3E4S5
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