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Crystal structure of protein of unknown function PG1108 from porphyromonas gingivalis W83

Analyse Crystal structure of protein of unknown function PG1108 from porphyromonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2H5N
Type: protein
Length: 501 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hypothetical protein PG_1108
UniProt: Q7MVF6
Ligands: MG
Pockets: 3 · best druggability 0.71

Structure

x-ray diffraction · 4 distinct chains · 68% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hypothetical protein PG_1108	protein	132	65% helix, 2% strand	Q7MVF6
B	Hypothetical protein PG_1108	protein	122	68% helix, 2% strand	Q7MVF6
C	Hypothetical protein PG_1108	protein	124	70% helix, 2% strand	Q7MVF6
D	Hypothetical protein PG_1108	protein	123	71% helix, 2% strand	Q7MVF6

Ligands and binding sites

MG · Magnesium ion · metal · 3 copies · chains A, B, C

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	992	0.71	0.75	108	empty
2	91	0.46	0.80	26	MG
3	78	0.34	0.75	17	empty

Interfaces

4 interfaces between chains.

C–D · 826 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 774 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 519 Å² buried · 1 hydrogen bond · protein-protein
B–D · 38 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

2H5N · Crystal Structure of Protein of Unknown Function PG1108 from Porphyromonas gingivalis W83 · 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 Q7MVF6
Elsewhere: RCSB PDB 2H5N · PDBe 2H5N · UniProt Q7MVF6

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