MolNFT v1 · #47122 · protein
Crystal structure of a dimeric ferredoxin-like protein (JCVI_PEP_1096672785533) from uncultured marine organism at 2.20 a resolution
2OP5 · Hypothetical protein: “Crystal structure of a dimeric ferredoxin-like protein (JCVI_PEP_1096672785533) from uncultured marine…”. X-ray diffraction, 9 pockets (best druggability 0.64). MolNFT v1 #47122 on GenesisL1: 3D structure…
- PDB
- 2OP5
- Type
- protein
- Length
- 659 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein
- Pockets
- 9 · best druggability 0.64
Structure
x-ray diffraction · 6 distinct chains · 41% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical protein | protein | 112 | 40% helix, 32% strand | — |
| B | Hypothetical protein | protein | 107 | 40% helix, 36% strand | — |
| C | Hypothetical protein | protein | 115 | 42% helix, 36% strand | — |
| D | Hypothetical protein | protein | 106 | 42% helix, 37% strand | — |
| E | Hypothetical protein | protein | 111 | 40% helix, 35% strand | — |
| F | Hypothetical protein | protein | 108 | 42% helix, 36% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 266 | 0.64 | 0.81 | 28 | empty |
| 2 | 260 | 0.61 | 0.79 | 21 | empty |
| 3 | 372 | 0.59 | 0.76 | 52 | empty |
| 4 | 171 | 0.58 | 0.81 | 22 | empty |
| 5 | 128 | 0.55 | 0.82 | 21 | empty |
Interfaces
7 interfaces between chains.
- C–D · 1618 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 1599 Ų buried · 36 hydrogen bonds · protein-protein
- E–F · 1536 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 619 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 242 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 modified (engineered).
Compared structures
- 2OP5 · Crystal structure of a dimeric ferredoxin-like protein (JCVI_PEP_1096672785533) 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
- Elsewhere: RCSB PDB 2OP5 · PDBe 2OP5
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