MolNFT v1 · #29356 · protein
Crystal structure of methylenetetrahydromethanopterin reductase (mer) in complex with coenzyme F420
1Z69 · Coenzyme F420-dependent N(5),N(10)…: “Crystal structure of methylenetetrahydromethanopterin reductase (mer) in complex with coenzyme F420”. X-ray diffraction, 3 ligands (F42, 1PG, CL), 11 pockets (best druggability 0.73). MolNFT v1…
- PDB
- 1Z69
- Type
- protein
- Length
- 1,308 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coenzyme F420-dependent N(5),N(10)- methylenetetrahydromethanopterin reductase
- EC
- 1.5.99.11
- Ligands
- F42, 1PG, CL
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Coenzyme F420-dependent N(5),N(10)- methylenetetrahydromethanopterin reductase (EC 1.5.99.11) | protein | 327 | 51% helix, 18% strand | — |
Ligands and binding sites
- F42 · Coenzyme F420 · ligand · 4 copies · chains A, B, C, D
- 1PG · 2-(2-{2-[2-(2-methoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethanol · ligand · chains C, D
- CL · Chloride ion · ion · 2 copies · chains B, C, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 720 | 0.73 | 0.78 | 71 | F42, 1PG |
| 2 | 590 | 0.70 | 0.78 | 59 | F42 |
| 3 | 534 | 0.69 | 0.79 | 33 | empty |
| 4 | 563 | 0.69 | 0.78 | 61 | F42 |
| 5 | 516 | 0.69 | 0.79 | 32 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1493 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1488 Ų buried · 28 hydrogen bonds · protein-protein
- B–D · 403 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 389 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 371 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 1Z69 · Crystal structure of methylenetetrahydromethanopterin reductase (Mer) in complex with… · 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
- Elsewhere: RCSB PDB 1Z69 · PDBe 1Z69
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