MolNFT v1 · #78628 · protein

Crystal structure of vopl C terminal domain

3SEO · Vopl C terminal domain protein: “Crystal structure of vopl C terminal domain”. X-ray diffraction, 1 ligand (CL), 5 pockets (best druggability 0.41). MolNFT v1 #78628 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3SEO
Type: protein
Length: 444 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vopl C terminal domain protein
UniProt: Q87GE5
Ligands: CL
Pockets: 5 · best druggability 0.41

Structure

x-ray diffraction · 2 distinct chains · 70% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vopl C terminal domain protein	protein	218	69% helix, 2% strand	Q87GE5
B	Vopl C terminal domain protein	protein	226	71% helix, 4% strand	Q87GE5

Ligands and binding sites

CL · Chloride ion · ion · 9 copies · chains A, B

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

Pockets

5 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	129	0.41	0.75	18	empty
2	116	0.38	0.74	22	empty
3	67	0.35	0.77	14	empty
4	69	0.35	0.77	16	empty
5	66	0.32	0.75	11	CL

Interfaces

1 interface between chains.

A–B · 1099 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

3SEO · Crystal structure of VopL C terminal domain · 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 Q87GE5
Elsewhere: RCSB PDB 3SEO · PDBe 3SEO · UniProt Q87GE5

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