MolNFT v1 · #123209 · protein

Crystal structure of LAE5, an ALPHA/BETA hydrolase enzyme from the metagenome of lake arreo, spain

5JD3: “Crystal structure of LAE5, an ALPHA/BETA hydrolase enzyme from the metagenome of lake arreo, spain”. X-ray diffraction, 2 ligands (CL, SO4), 12 pockets (best druggability 0.75). MolNFT v1 #123209 on GenesisL1: 3D structure, binding…

PDB: 5JD3
Type: protein
Length: 1,743 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: LAE5
Ligands: CL, SO4
Pockets: 12 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 50% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, H	LAE5	protein	218	50% helix, 11% strand	—
G	LAE5	protein	217	51% helix, 11% strand	—

Ligands and binding sites

CL · Chloride ion · ion · 4 copies · chains A, C, B, E, H
SO4 · Sulfate ion · ion · chains A, B
PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, D, B, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	829	0.75	0.79	84	empty
2	715	0.75	0.80	70	empty
3	649	0.73	0.80	76	empty
4	683	0.73	0.80	76	PEG
5	758	0.73	0.79	78	PEG

Interfaces

15 interfaces between chains.

E–H · 1211 Å² buried · 9 hydrogen bonds · protein-protein
A–D · 1188 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 1178 Å² buried · 9 hydrogen bonds · protein-protein
A–F · 843 Å² buried · 6 hydrogen bonds · protein-protein
C–E · 843 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

5JD3 · Crystal structure of LAE5, an alpha/beta hydrolase enzyme from the metagenome of Lake… · 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
Elsewhere: RCSB PDB 5JD3 · PDBe 5JD3

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