MolNFT v1 · #123185 · protein

Crystal structure of oscebip

5JCD · Chitin elicitor-binding protein: “Crystal structure of oscebip”. X-ray diffraction, 1 ligand (NAG), 3 pockets (best druggability 0.54). MolNFT v1 #123185 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5JCD
Type: protein
Length: 582 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chitin elicitor-binding protein
UniProt: Q8H8C7
Ligands: NAG
Pockets: 3 · best druggability 0.54

Structure

x-ray diffraction · 2 distinct chains · 23% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Chitin elicitor-binding protein	protein	195	24% helix, 26% strand	Q8H8C7
C	Chitin elicitor-binding protein	protein	192	22% helix, 28% strand	Q8H8C7

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	330	0.54	0.75	41	empty
2	308	0.54	0.74	31	empty
3	62	0.31	0.75	15	empty

Interfaces

2 interfaces between chains.

A–B · 232 Å² buried · 1 hydrogen bond · protein-protein
B–C · 75 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

5JCD · Crystal structure of OsCEBiP · the same entry in another collection · chain A against A, TM-score 1.00
Q8H8C7 · AlphaFold monomer V2.0 prediction for chitin elicitor-binding protein (Q8H8C7) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 Q8H8C7
Elsewhere: RCSB PDB 5JCD · PDBe 5JCD · UniProt Q8H8C7

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