MolNFT v1 · #152777 · protein

Crystal structure of a wild type endolysin lysime-EF1

6IST: “Crystal structure of a wild type endolysin lysime-EF1”. X-ray diffraction, 1 ligand (CA), 3 pockets (best druggability 0.72). MolNFT v1 #152777 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6IST
Type: protein
Length: 423 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lysin
UniProt: S5MRN1
Ligands: CA
Pockets: 3 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 28% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	Lysin	protein	70	31% helix, 30% strand	S5MRN1
C	Lysin	protein	213	27% helix, 27% strand	S5MRN1

Ligands and binding sites

CA · Calcium ion · metal · chains 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	887	0.72	0.76	53	empty
2	296	0.52	0.74	32	empty
3	109	0.47	0.79	27	empty

Interfaces

4 interfaces between chains.

C–D · 732 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 695 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 691 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 688 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

6IST · Crystal structure of a wild type endolysin LysIME-EF1 · 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 S5MRN1
Elsewhere: RCSB PDB 6IST · PDBe 6IST · UniProt S5MRN1

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