MolNFT v1 · #104207 · protein

Crystal structure of mgs-M2, an ALPHA/BETA hydrolase enzyme from a medee basin deep-sea metagenome library

4Q3L: “Crystal structure of mgs-M2, an ALPHA/BETA hydrolase enzyme from a medee basin deep-sea metagenome library”. X-ray diffraction, 20 pockets (best druggability 0.84). MolNFT v1 #104207 on GenesisL1: 3D structure, binding sites and…

PDB: 4Q3L
Type: protein
Length: 2,216 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mgs-M2
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 3 distinct chains · 46% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, E, F	Mgs-M2	protein	275	49% helix, 18% strand	—
B, H	Mgs-M2	protein	280	46% helix, 18% strand	—
C, G	Mgs-M2	protein	278	44% helix, 17% strand	—

Ligands and binding sites

GOL · Glycerol · additive · 2 copies · chains B, G

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

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	642	0.84	0.88	68	empty
2	581	0.83	0.89	85	empty
3	376	0.80	0.89	48	empty
4	395	0.80	0.88	60	empty
5	382	0.79	0.88	52	empty

Interfaces

12 interfaces between chains.

A–C · 1713 Å² buried · 25 hydrogen bonds · protein-protein
B–D · 1680 Å² buried · 23 hydrogen bonds · protein-protein
E–H · 1660 Å² buried · 25 hydrogen bonds · protein-protein
F–G · 1654 Å² buried · 23 hydrogen bonds · protein-protein
F–H · 1351 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

4Q3L · Crystal structure of MGS-M2, an alpha/beta hydrolase enzyme from a Medee basin deep-sea… · 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 4Q3L · PDBe 4Q3L

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