MolNFT v1 · #127324 · protein

Crystal structure of pdf from the vibrio parahaemolyticus bacteriophage VP16T - crystal form I

5MTC · Putative uncharacterized protein ORF60T: “Crystal structure of pdf from the vibrio parahaemolyticus bacteriophage VP16T - crystal form I”. X-ray diffraction, 2 ligands (ZN, NI), 3 pockets (best druggability 0.67). MolNFT v1 #127324…

PDB: 5MTC
Type: protein
Length: 274 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative uncharacterized protein ORF60T
UniProt: Q6VT21
Ligands: ZN, NI
Pockets: 3 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 26% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Putative uncharacterized protein ORF60T	protein	137	26% helix, 35% strand	Q6VT21

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A, B
NI · Nickel (II) ion · metal · 2 copies · 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	390	0.67	0.80	41	empty
2	87	0.43	0.79	17	empty
3	80	0.41	0.79	17	empty

Interfaces

1 interface between chains.

A–B · 334 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

5MTC · Crystal structure of PDF from the Vibrio parahaemolyticus bacteriophage VP16T - crystal… · the same entry in another collection · chain A against A, TM-score 1.00

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 Q6VT21
Elsewhere: RCSB PDB 5MTC · PDBe 5MTC · UniProt Q6VT21

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