MolNFT v1 · #110048 · protein
Crystal structure of nika from staphylococcus aureus in complex with ni-(L-HIS)(2-methyl-thiazolidine dicarboxylate) (co-crystallization with NI(II) and cddeltahis medium supernatant)
4XKR · Nickel ABC transporter substrate-binding protein: “Crystal structure of nika from staphylococcus aureus in complex with ni-(L-HIS)(2-methyl-thiazolidine…”. X-ray diffraction, 4 ligands (HIS, 41K, NI), 5 pockets (best druggability…
- PDB
- 4XKR
- Type
- protein
- Length
- 464 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, 41K, NI, NA
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nickel ABC transporter substrate-binding protein | protein | 464 | 28% helix, 24% strand | W6DY02 |
Ligands and binding sites
- HIS · Histidine · ligand · chains A
- 41K · (2R,4R)-2-methyl-1,3-thiazolidine-2,4-dicarboxylic acid · ligand · chains A
- NI · Nickel (II) ion · metal · chains A
- NA · Sodium ion · metal · chains A
- GOL · Glycerol · additive · 18 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 | 723 | 0.81 | 0.85 | 79 | NI, HIS, 41K, GOL, NA |
| 2 | 159 | 0.70 | 0.89 | 31 | GOL |
| 3 | 103 | 0.46 | 0.80 | 22 | GOL |
| 4 | 140 | 0.41 | 0.74 | 25 | empty |
| 5 | 69 | 0.32 | 0.75 | 17 | GOL |
Compared structures
- 4XKR · Crystal structure of NikA from Staphylococcus aureus in complex with… · 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 4XKR · PDBe 4XKR · UniProt W6DY02
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