Research workbench
Structure of T. brucei RRP44 pin domain
Analyse Structure of T. brucei RRP44 pin domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MD3
- Type
- protein
- Length
- 1,036 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RRP44P homologue
- UniProt
- Q95Z12
- Ligands
- MN, ZN, CL
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RRP44P homologue | protein | 170 | 44% helix, 14% strand | Q95Z12 |
| B | RRP44P homologue | protein | 174 | 43% helix, 14% strand | Q95Z12 |
| C | RRP44P homologue | protein | 180 | 45% helix, 14% strand | Q95Z12 |
| D | RRP44P homologue | protein | 165 | 45% helix, 15% strand | Q95Z12 |
| E | RRP44P homologue | protein | 168 | 45% helix, 14% strand | Q95Z12 |
| F | RRP44P homologue | protein | 179 | 46% helix, 13% strand | Q95Z12 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 12 copies · chains A, B, C, D, E, F
- ZN · Zinc ion · metal · 12 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 11 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1087 | 0.82 | 0.83 | 93 | CL |
| 2 | 899 | 0.80 | 0.82 | 76 | CL |
| 3 | 863 | 0.79 | 0.82 | 71 | empty |
| 4 | 1042 | 0.79 | 0.81 | 101 | empty |
| 5 | 306 | 0.67 | 0.82 | 45 | empty |
Interfaces
11 interfaces between chains.
- C–F · 1598 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 1593 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 1586 Ų buried · 13 hydrogen bonds · protein-protein
- C–E · 567 Ų buried · 3 hydrogen bonds · protein-protein
- D–F · 559 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6MD3 · Structure of T. brucei RRP44 PIN domain · the same entry in another collection · chain B against B, 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 Q95Z12
- Elsewhere: RCSB PDB 6MD3 · PDBe 6MD3 · UniProt Q95Z12
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