Research workbench
Structure of atopobium parvulum sufs K235R
Analyse Structure of atopobium parvulum sufs K235R in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TLP
- Type
- protein
- Length
- 2,365 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cysteine desulfurase
- EC
- 2.8.1.7
- UniProt
- C8W9P2
- Ligands
- PLG
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cysteine desulfurase (EC 2.8.1.7) | protein | 391 | 45% helix, 15% strand | C8W9P2 |
| B | Cysteine desulfurase (EC 2.8.1.7) | protein | 393 | 46% helix, 16% strand | C8W9P2 |
| C | Cysteine desulfurase (EC 2.8.1.7) | protein | 392 | 46% helix, 16% strand | C8W9P2 |
| D | Cysteine desulfurase (EC 2.8.1.7) | protein | 398 | 45% helix, 16% strand | C8W9P2 |
| E | Cysteine desulfurase (EC 2.8.1.7) | protein | 395 | 46% helix, 16% strand | C8W9P2 |
| F | Cysteine desulfurase (EC 2.8.1.7) | protein | 396 | 46% helix, 16% strand | C8W9P2 |
Ligands and binding sites
- PLG · N-glycine-[3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-yl-methane] · ligand · 6 copies · chains A, B, C, E, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 791 | 0.78 | 0.82 | 69 | empty |
| 2 | 728 | 0.78 | 0.82 | 61 | empty |
| 3 | 797 | 0.77 | 0.81 | 67 | empty |
| 4 | 840 | 0.71 | 0.76 | 75 | empty |
| 5 | 61 | 0.70 | 0.97 | 22 | empty |
Interfaces
7 interfaces between chains.
- C–E · 1761 Ų buried · 35 hydrogen bonds · protein-protein
- A–D · 533 Ų buried · 7 hydrogen bonds · protein-protein
- B–E · 528 Ų buried · 10 hydrogen bonds · protein-protein
- C–F · 523 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 193 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7TLP · Structure of Atopobium parvulum SufS K235R · 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 C8W9P2
- Elsewhere: RCSB PDB 7TLP · PDBe 7TLP · UniProt C8W9P2
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