MolNFT v1 · #50519 · protein

Crystal structure of S.CEREVISIAE VTA1 C-terminal domain

2RKL · Vacuolar protein sorting-associated protein VTA1: “Crystal structure of S.CEREVISIAE VTA1 C-terminal domain”. X-ray diffraction, 2 pockets (best druggability 0.62). MolNFT v1 #50519 on GenesisL1: 3D structure, binding sites and…

PDB: 2RKL
Type: protein
Length: 294 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vacuolar protein sorting-associated protein VTA1
UniProt: Q06263
Pockets: 2 · best druggability 0.62

Structure

x-ray diffraction · 5 distinct chains · 87% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Vacuolar protein sorting-associated protein VTA1	protein	53	85% helix, 0% strand	Q06263
B	Vacuolar protein sorting-associated protein VTA1	protein	50	88% helix, 0% strand	Q06263
D	Vacuolar protein sorting-associated protein VTA1	protein	42	86% helix, 0% strand	Q06263
E	Vacuolar protein sorting-associated protein VTA1	protein	44	86% helix, 0% strand	Q06263
F	Vacuolar protein sorting-associated protein VTA1	protein	52	88% helix, 0% strand	Q06263

Ligands and binding sites

MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains B, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	369	0.62	0.78	42	MPD
2	154	0.42	0.75	19	empty

Interfaces

8 interfaces between chains.

C–D · 998 Å² buried · 8 hydrogen bonds · protein-protein
E–F · 988 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 988 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 294 Å² buried · 4 hydrogen bonds · protein-protein
D–E · 156 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

2RKL · Crystal Structure of S.cerevisiae Vta1 C-terminal domain · the same entry in another collection · chain F against F, TM-score 1.00
Q06263 · AlphaFold monomer V2.0 prediction for vacuolar protein sorting- associated protein VTA1… · a predicted model of the same protein · chain D against A, TM-score 0.95

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 Q06263
Elsewhere: RCSB PDB 2RKL · PDBe 2RKL · UniProt Q06263

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