MolNFT v1 · #116671 · protein

Crystal structure of calcium-loaded S100B bound to SBI29

5DKR · Protein S100-B: “Crystal structure of calcium-loaded S100B bound to SBI29”. X-ray diffraction, 2 ligands (5CZ, CA). MolNFT v1 #116671 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5DKR
Type: protein
Length: 179 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein S100-B
UniProt: P02638
Ligands: 5CZ, CA

Structure

x-ray diffraction · 2 distinct chains · 64% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein S100-B	protein	89	64% helix, 2% strand	P02638
B	Protein S100-B	protein	90	64% helix, 4% strand	P02638

Ligands and binding sites

5CZ · 2-[4-(4-carbamimidoylphenoxy)phenyl]-1H-indole-6-carboximidamide · ligand · chains A, B
CA · Calcium ion · metal · 5 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Interfaces

1 interface between chains.

A–B · 1474 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

5DKR · Crystal Structure of Calcium-loaded S100B bound to SBi29 · the same entry in another collection · chain A against A, TM-score 1.00
P02638 · AlphaFold monomer V2.0 prediction for protein S100-B (P02638) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P02638
Elsewhere: RCSB PDB 5DKR · PDBe 5DKR · UniProt P02638

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