MolNFT v1 · #167274 · protein

Crystal structure of human delta protocadherin 17 EC1-EC4

6VFT · Protocadherin-17: “Crystal structure of human delta protocadherin 17 EC1-EC4”. X-ray diffraction, 5 ligands (NAG, MAN, FUC), 20 pockets (best druggability 0.77). MolNFT v1 #167274 on GenesisL1: 3D structure, binding sites and…

PDB: 6VFT
Type: protein
Length: 1,665 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protocadherin-17
UniProt: O14917
Ligands: NAG, MAN, FUC, BMA, CA
Pockets: 20 · best druggability 0.77

Structure

x-ray diffraction · 4 distinct chains · 6% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protocadherin-17	protein	413	7% helix, 48% strand	O14917
B	Protocadherin-17	protein	414	7% helix, 48% strand	O14917
C	Protocadherin-17	protein	420	6% helix, 48% strand	O14917
D	Protocadherin-17	protein	418	6% helix, 47% strand	O14917

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 19 copies · chains A, B, C, D
MAN · alpha-D-mannopyranose · sugar · 9 copies · chains A, B, C, D
FUC · alpha-L-fucopyranose · sugar · 5 copies · chains A
BMA · beta-D-mannopyranose · sugar · 4 copies
CA · Calcium ion · metal · 40 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1123	0.77	0.79	110	empty
2	969	0.73	0.77	98	empty
3	650	0.73	0.80	56	empty
4	529	0.71	0.80	70	empty
5	313	0.62	0.79	45	empty

Interfaces

6 interfaces between chains.

A–B · 1640 Å² buried · 17 hydrogen bonds · protein-protein
C–D · 1513 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 1190 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 1119 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 645 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 19 glycan, 4 disulfide (N-glycosylation, O-glycosylation, disulfide).

Compared structures

6VFT · Crystal structure of human delta protocadherin 17 EC1-EC4 · the same entry in another collection · chain D against D, TM-score 1.00
O14917 · AlphaFold monomer V2.0 prediction for protocadherin-17 (O14917) · a predicted model of the same protein · chain B against A, TM-score 0.94

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 O14917
Elsewhere: RCSB PDB 6VFT · PDBe 6VFT · UniProt O14917

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