MolNFT v1 · #159044 · protein

Crystal structure of VASH1-svbp complex bound with epoy

6OCG · Tubulinyl-tyr carboxypeptidase 1: “Crystal structure of VASH1-svbp complex bound with epoy”. X-ray diffraction, 2 ligands (BJL, CL), 3 pockets (best druggability 0.54). MolNFT v1 #159044 on GenesisL1: 3D structure, binding sites and…

PDB: 6OCG
Type: protein
Length: 273 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tubulinyl-tyr carboxypeptidase 1; Small vasohibin-binding protein
EC: 3.4.17.17
UniProt: Q7L8A9, Q8N300
Ligands: BJL, CL
Pockets: 3 · best druggability 0.54

Structure

x-ray diffraction · 2 distinct chains · 46% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tubulinyl-tyr carboxypeptidase 1 (EC 3.4.17.17)	protein	247	41% helix, 21% strand	Q7L8A9
B	Small vasohibin-binding protein	protein	26	88% helix, 0% strand	Q8N300

Ligands and binding sites

BJL · N-[(3R)-4-ethoxy-3-hydroxy-4-oxobutanoyl]-L-tyrosine · ligand · chains A
CL · Chloride ion · ion · chains A
GOL · Glycerol · additive · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	282	0.54	0.76	27	BJL
2	82	0.42	0.79	24	empty
3	59	0.27	0.73	14	empty

Interfaces

1 interface between chains.

A–B · 1182 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

6OCG · Crystal structure of VASH1-SVBP complex bound with EpoY · the same entry in another collection · chain A against A, TM-score 1.00
Q7L8A9 · AlphaFold monomer V2.0 prediction for tubulinyl-tyr carboxypeptidase 1 (Q7L8A9) · a predicted model of the same protein · chain A against A, TM-score 0.99
Q8N300 · AlphaFold monomer V2.0 prediction for small vasohibin-binding protein (Q8N300) · a predicted model of the same protein · chain B against A, TM-score 0.74

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 Q7L8A9
Every structure of UniProt Q8N300
Elsewhere: RCSB PDB 6OCG · PDBe 6OCG · UniProt Q7L8A9 · UniProt Q8N300

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