MolNFT v1 · #163941 · protein

Epidermicin antimicrobial protein from staphylococcus epidermidis

6SIF · Epidermicin locus structural protein: “Epidermicin antimicrobial protein from staphylococcus epidermidis”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.69). MolNFT v1 #163941 on GenesisL1: 3D structure, binding…

PDB: 6SIF
Type: protein
Length: 401 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Epidermicin locus structural protein
UniProt: H9BG66
Ligands: SO4
Pockets: 5 · best druggability 0.69

Structure

x-ray diffraction · 4 distinct chains · 82% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, F	Epidermicin locus structural protein	protein	51	82% helix, 2% strand	H9BG66
D	Epidermicin locus structural protein	protein	50	82% helix, 0% strand	H9BG66
E, H	Epidermicin locus structural protein	protein	50	82% helix, 2% strand	H9BG66
G	Epidermicin locus structural protein	protein	47	81% helix, 0% strand	H9BG66

Ligands and binding sites

SO4 · Sulfate ion · ion · 8 copies · chains B, G, D, E, F, H

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	492	0.69	0.79	54	empty
2	402	0.67	0.79	41	empty
3	199	0.44	0.73	24	empty
4	84	0.36	0.75	10	empty
5	58	0.33	0.76	13	empty

Interfaces

14 interfaces between chains.

B–C · 388 Å² buried · 0 hydrogen bonds · protein-protein
D–F · 377 Å² buried · 0 hydrogen bonds · protein-protein
A–G · 332 Å² buried · 1 hydrogen bond · protein-protein
E–H · 256 Å² buried · 1 hydrogen bond · protein-protein
A–E · 188 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

6SIF · Epidermicin antimicrobial protein from Staphylococcus epidermidis · the same entry in another collection · chain E against E, 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 H9BG66
Elsewhere: RCSB PDB 6SIF · PDBe 6SIF · UniProt H9BG66

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