Research workbench
Crystal structure of TT0321 from thermus thermophilus HB8
Analyse Crystal structure of TT0321 from thermus thermophilus HB8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2D1Y
- Type
- protein
- Length
- 970 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein TT0321
- UniProt
- Q5SLC4
- Ligands
- NAD
- Pockets
- 13 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical protein TT0321 | protein | 240 | 49% helix, 18% strand | Q5SLC4 |
| B | Hypothetical protein TT0321 | protein | 242 | 50% helix, 17% strand | Q5SLC4 |
| C | Hypothetical protein TT0321 | protein | 248 | 50% helix, 17% strand | Q5SLC4 |
| D | Hypothetical protein TT0321 | protein | 240 | 49% helix, 18% strand | Q5SLC4 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 889 | 0.87 | 0.88 | 54 | empty |
| 2 | 612 | 0.76 | 0.82 | 51 | NAD |
| 3 | 751 | 0.74 | 0.79 | 60 | NAD |
| 4 | 717 | 0.74 | 0.79 | 60 | NAD |
| 5 | 652 | 0.73 | 0.79 | 47 | NAD |
Interfaces
6 interfaces between chains.
- A–D · 1612 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 1612 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1384 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 1383 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 489 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2D1Y · Crystal structure of TT0321 from Thermus thermophilus HB8 · 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 Q5SLC4
- Elsewhere: RCSB PDB 2D1Y · PDBe 2D1Y · UniProt Q5SLC4
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