MolNFT v1 · #54269 · protein
Crystal structure of streptococcus suis dpr with nickel
2XJO · DNA protection during starvation protein: “Crystal structure of streptococcus suis dpr with nickel”. X-ray diffraction, 3 ligands (NI, CA, CL), 20 pockets (best druggability 0.75). MolNFT v1 #54269 on GenesisL1: 3D structure…
- PDB
- 2XJO
- Type
- protein
- Length
- 1,811 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
- P0CB53
- Ligands
- NI, CA, CL
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | DNA protection during starvation protein (EC 1.16.-.-) | protein | 150 | 75% helix, 0% strand | P0CB53 |
| B, E, F, H, I, J | DNA protection during starvation protein (EC 1.16.-.-) | protein | 151 | 75% helix, 0% strand | P0CB53 |
| D, K, L | DNA protection during starvation protein (EC 1.16.-.-) | protein | 152 | 75% helix, 0% strand | P0CB53 |
| G | DNA protection during starvation protein (EC 1.16.-.-) | protein | 149 | 76% helix, 0% strand | P0CB53 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 12 copies · chains A, C, B, D, E, G, F, H, I, K, J, L
- CA · Calcium ion · metal · 7 copies · chains B, D, F, I, J, H, K
- CL · Chloride ion · ion · 6 copies · chains B, L, D, A, E, G, I, J
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 4 copies · chains B, F, J, D, G, I, A, H, K, C, E, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 112 | 0.75 | 0.95 | 24 | empty |
| 2 | 99 | 0.75 | 0.96 | 18 | empty |
| 3 | 104 | 0.75 | 0.95 | 20 | empty |
| 4 | 96 | 0.74 | 0.96 | 23 | empty |
| 5 | 98 | 0.74 | 0.95 | 20 | empty |
Interfaces
30 interfaces between chains.
- E–G · 1238 Ų buried · 17 hydrogen bonds · protein-protein
- I–K · 1231 Ų buried · 18 hydrogen bonds · protein-protein
- J–L · 1212 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1205 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1204 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 2XJO · Crystal structure of Streptococcus suis Dpr with nickel · the same entry in another collection · chain L against L, 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 P0CB53
- Elsewhere: RCSB PDB 2XJO · PDBe 2XJO · UniProt P0CB53
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