MolNFT v1 · #167277 · protein

Crystal structure of human delta protocadherin 10 EC1-EC4

6VFW: “Crystal structure of human delta protocadherin 10 EC1-EC4”. X-ray diffraction, 5 ligands (MAN, NAG, BMA). MolNFT v1 #167277 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6VFW
Type: protein
Length: 2,120 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
UniProt: Q9P2E7
Ligands: MAN, NAG, BMA, FUC, CA

Structure

x-ray diffraction · 5 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	—	protein	423	—	Q9P2E7
B	—	protein	423	—	Q9P2E7
C	—	protein	429	—	Q9P2E7
D	—	protein	423	—	Q9P2E7
E	—	protein	422	—	Q9P2E7

Ligands and binding sites

MAN · alpha-D-mannopyranose · sugar · 20 copies · chains D, A, B, C, E
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B, C, D, E
BMA · beta-D-mannopyranose · sugar · 5 copies
FUC · alpha-L-fucopyranose · sugar · 5 copies
CA · Calcium ion · metal · 45 copies · chains A, B, C, D, E

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

Compared structures

6VFW · Crystal structure of human delta protocadherin 10 EC1-EC4 · the same entry in another collection · chain E against E, TM-score 1.00
Q9P2E7 · AlphaFold monomer V2.0 prediction for protocadherin-10 (Q9P2E7) · a predicted model of the same protein · chain E against A, TM-score 0.97

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 Q9P2E7
Elsewhere: RCSB PDB 6VFW · PDBe 6VFW · UniProt Q9P2E7

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