Research workbench
Crystal structure of a cupin-like protein (TM1010) from thermotoga maritima MSB8 at 1.90 a resolution
Analyse Crystal structure of a cupin-like protein (TM1010) from thermotoga maritima… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2F4P
- Type
- protein
- Length
- 532 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein TM1010
- Ligands
- UNL
- Pockets
- 8 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical protein TM1010 | protein | 134 | 10% helix, 45% strand | — |
| B | Hypothetical protein TM1010 | protein | 132 | 8% helix, 45% strand | — |
| C, D | Hypothetical protein TM1010 | protein | 133 | 8% helix, 47% strand | — |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 385 | 0.61 | 0.77 | 54 | empty |
| 2 | 196 | 0.55 | 0.79 | 30 | UNL |
| 3 | 179 | 0.55 | 0.79 | 26 | UNL |
| 4 | 169 | 0.54 | 0.79 | 25 | UNL |
| 5 | 196 | 0.53 | 0.78 | 29 | UNL |
Interfaces
6 interfaces between chains.
- A–B · 953 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 945 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 184 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 110 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 101 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 2F4P · Crystal structure of a cupin-like protein (tm1010) from thermotoga maritima msb8 at 1.90… · 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 2F4P · PDBe 2F4P
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