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Crystal structure of synbindin

Analyse Crystal structure of synbindin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2ZMV
Type: protein
Length: 405 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Trafficking protein particle complex subunit 4
UniProt: Q9Y296
Pockets: 6 · best druggability 0.68

Structure

x-ray diffraction · 2 distinct chains · 24% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Trafficking protein particle complex subunit 4	protein	202	27% helix, 32% strand	Q9Y296
B	Trafficking protein particle complex subunit 4	protein	203	22% helix, 31% strand	Q9Y296

Pockets

6 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	594	0.68	0.77	61	empty
2	161	0.58	0.82	22	empty
3	137	0.45	0.77	25	empty
4	145	0.42	0.75	22	empty
5	78	0.41	0.79	18	empty

Interfaces

1 interface between chains.

A–B · 900 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

2ZMV · Crystal structure of Synbindin · the same entry in another collection · chain B against B, TM-score 1.00
Q9Y296 · AlphaFold monomer V2.0 prediction for trafficking protein particle complex subunit 4… · a predicted model of the same protein · chain B against A, TM-score 0.84

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 Q9Y296
Elsewhere: RCSB PDB 2ZMV · PDBe 2ZMV · UniProt Q9Y296

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