MolNFT v1 · #51225 · protein
Terbium binding in streptococcus suis dpr protein
2V15 · DNA protection during starvation protein: “Terbium binding in streptococcus suis dpr protein”. X-ray diffraction, 3 ligands (TB, CA, CL), 20 pockets (best druggability 0.75). MolNFT v1 #51225 on GenesisL1: 3D structure, binding…
- PDB
- 2V15
- Type
- protein
- Length
- 1,834 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA protection during starvation protein
- EC
- 1.16.-.-
- UniProt
- Q4A3W3
- Ligands
- TB, CA, CL
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E | DNA protection during starvation protein (EC 1.16.-.-) | protein | 151 | 76% helix, 0% strand | Q4A3W3 |
| D, F, H, J, K, L | DNA protection during starvation protein (EC 1.16.-.-) | protein | 152 | 75% helix, 0% strand | Q4A3W3 |
| G | DNA protection during starvation protein (EC 1.16.-.-) | protein | 165 | 68% helix, 0% strand | Q4A3W3 |
| I | DNA protection during starvation protein (EC 1.16.-.-) | protein | 153 | 75% helix, 0% strand | Q4A3W3 |
Ligands and binding sites
- TB · Terbium(iii) ion · metal · 12 copies · chains A, C, B, D, E, G, F, H, I, K, J, L
- CA · Calcium ion · metal · 4 copies · chains B, G, H, K
- CL · Chloride ion · ion · 10 copies · chains A, C, H, E, B, D, F, G, L, I, K, J
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 4 copies · chains D, G, I, C, E, L, B, F, J, A, H, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 112 | 0.75 | 0.95 | 23 | empty |
| 2 | 110 | 0.75 | 0.95 | 19 | empty |
| 3 | 115 | 0.74 | 0.94 | 26 | empty |
| 4 | 201 | 0.70 | 0.87 | 32 | empty |
| 5 | 213 | 0.70 | 0.86 | 32 | empty |
Interfaces
30 interfaces between chains.
- J–L · 1194 Ų buried · 19 hydrogen bonds · protein-protein
- F–H · 1192 Ų buried · 20 hydrogen bonds · protein-protein
- I–K · 1185 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 1178 Ų buried · 20 hydrogen bonds · protein-protein
- E–G · 1177 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 2V15 · Terbium binding in Streptococcus suis Dpr protein · 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 Q4A3W3
- Elsewhere: RCSB PDB 2V15 · PDBe 2V15 · UniProt Q4A3W3
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