Research workbench
Crystal structure of nika from staphylococcus aureus in complex with NI(L-HIS)2 (co-crystallization with NI(II) and bhi medium supernatant)
Analyse Crystal structure of nika from staphylococcus aureus in complex with NI(L-HIS)2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XKP
- Type
- protein
- Length
- 465 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nickel ABC transporter substrate-binding protein
- UniProt
- W6DY02
- Ligands
- HIS, NI
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nickel ABC transporter substrate-binding protein | protein | 465 | 28% helix, 25% strand | W6DY02 |
Ligands and binding sites
- HIS · Histidine · ligand · 2 copies · chains A
- NI · Nickel (II) ion · metal · chains A
- GOL · Glycerol · additive · 9 copies · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 651 | 0.80 | 0.85 | 67 | NI, HIS, GOL |
| 2 | 159 | 0.70 | 0.89 | 30 | empty |
| 3 | 111 | 0.47 | 0.80 | 23 | GOL |
| 4 | 127 | 0.40 | 0.74 | 27 | empty |
| 5 | 57 | 0.28 | 0.74 | 15 | empty |
Compared structures
- 4XKP · Crystal structure of NikA from Staphylococcus aureus in complex with Ni(L-His)2… · 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 W6DY02
- Elsewhere: RCSB PDB 4XKP · PDBe 4XKP · UniProt W6DY02
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