MolNFT v1 · #51771 · protein

DEBP

2VHA · Periplasmic binding transport protein: “DEBP”. X-ray diffraction, 1 ligand (GLU), 3 pockets (best druggability 0.45). MolNFT v1 #51771 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2VHA
Type: protein
Length: 552 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Periplasmic binding transport protein
UniProt: Q83S74
Ligands: GLU
Pockets: 3 · best druggability 0.45

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Periplasmic binding transport protein	protein	276	38% helix, 24% strand	Q83S74

Ligands and binding sites

GLU · Glutamic acid · ligand · 2 copies · chains A, B
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	165	0.45	0.75	24	empty
2	63	0.31	0.74	15	empty
3	56	0.28	0.74	17	empty

Interfaces

1 interface between chains.

A–B · 776 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

2VHA · DEBP · 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 Q83S74
Elsewhere: RCSB PDB 2VHA · PDBe 2VHA · UniProt Q83S74

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