MolNFT v1 · #111822 · protein
Mimivirus R135 (residues 51-702)
4Z25 · Putative gmc-type oxidoreductase R135: “Mimivirus R135 (residues 51-702)”. X-ray diffraction, 1 ligand (FAD), 20 pockets (best druggability 0.87). MolNFT v1 #111822 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4Z25
- Type
- protein
- Length
- 7,788 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative gmc-type oxidoreductase R135
- EC
- 1.-.-.-
- UniProt
- Q5UPL2
- Ligands
- FAD
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Putative gmc-type oxidoreductase R135 (EC 1.-.-.-) | protein | 649 | 33% helix, 20% strand | Q5UPL2 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
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 | 899 | 0.87 | 0.89 | 107 | FAD |
| 2 | 1140 | 0.85 | 0.86 | 117 | FAD |
| 3 | 475 | 0.84 | 0.91 | 60 | FAD |
| 4 | 365 | 0.84 | 0.93 | 57 | FAD |
| 5 | 376 | 0.84 | 0.93 | 58 | FAD |
Interfaces
17 interfaces between chains.
- A–C · 2573 Ų buried · 38 hydrogen bonds · protein-protein
- B–D · 2530 Ų buried · 44 hydrogen bonds · protein-protein
- G–K · 2519 Ų buried · 33 hydrogen bonds · protein-protein
- F–J · 2502 Ų buried · 36 hydrogen bonds · protein-protein
- E–I · 2491 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 4Z25 · Mimivirus R135 (residues 51-702) · 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 Q5UPL2
- Elsewhere: RCSB PDB 4Z25 · PDBe 4Z25 · UniProt Q5UPL2
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