Research workbench
Crystal structure of the tudor domain of human TDRD3 in complex with an anti-TDRD3 Fab
Analyse Crystal structure of the tudor domain of human TDRD3 in complex with an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PNW
- Type
- protein
- Length
- 3,932 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab light chain; Fab heavy chain; Tudor domain-containing protein 3
- UniProt
- Q9H7E2
- Ligands
- UNX
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 13 distinct chains · 8% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J, P | Fab light chain | protein | 213 | 6% helix, 51% strand | — |
| B, T | Fab heavy chain | protein | 225 | 9% helix, 51% strand | — |
| C | Tudor domain-containing protein 3 | protein | 60 | 12% helix, 48% strand | Q9H7E2 |
| E, N | Fab heavy chain | protein | 226 | 11% helix, 52% strand | — |
| F | Tudor domain-containing protein 3 | protein | 53 | 6% helix, 51% strand | Q9H7E2 |
| H, K, Q | Fab heavy chain | protein | 218 | 10% helix, 50% strand | — |
| I | Tudor domain-containing protein 3 | protein | 55 | 5% helix, 53% strand | Q9H7E2 |
| L, U | Tudor domain-containing protein 3 | protein | 54 | 6% helix, 50% strand | Q9H7E2 |
| M, S | Fab light chain | protein | 214 | 6% helix, 51% strand | — |
| O, R | Tudor domain-containing protein 3 | protein | 61 | 10% helix, 48% strand | Q9H7E2 |
| V | Fab light chain | protein | 212 | 6% helix, 51% strand | — |
| W | Fab heavy chain | protein | 220 | 8% helix, 52% strand | — |
| X | Tudor domain-containing protein 3 | protein | 53 | 6% helix, 53% strand | Q9H7E2 |
Ligands and binding sites
- UNX · Unknown atom or ion · ion · 143 copies · chains A, B, K, C, D, E, F, G, I, H, J, M, N, W, P, Q, R, S, T, V
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 879 | 0.81 | 0.83 | 69 | UNX |
| 2 | 942 | 0.78 | 0.80 | 85 | empty |
| 3 | 1119 | 0.73 | 0.77 | 114 | UNX |
| 4 | 751 | 0.71 | 0.77 | 69 | UNX |
| 5 | 479 | 0.64 | 0.77 | 60 | UNX |
Interfaces
48 interfaces between chains.
- J–K · 1837 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 1833 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1827 Ų buried · 14 hydrogen bonds · protein-protein
- M–N · 1814 Ų buried · 13 hydrogen bonds · protein-protein
- P–Q · 1810 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 disulfide (disulfide).
Compared structures
- 3PNW · Crystal Structure of the tudor domain of human TDRD3 in complex with an anti-TDRD3 FAB · the same entry in another collection · chain O against O, 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 Q9H7E2
- Elsewhere: RCSB PDB 3PNW · PDBe 3PNW · UniProt Q9H7E2
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