MolNFT v1 · #72708 · protein

Crystal structure of lipase from gibberella zeae

3NGM · Extracellular lipase: “Crystal structure of lipase from gibberella zeae”. X-ray diffraction, 11 pockets (best druggability 0.77). MolNFT v1 #72708 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3NGM
Type: protein
Length: 1,188 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Extracellular lipase
EC: 3.1.1.3
UniProt: Q6WER3
Pockets: 11 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Extracellular lipase (EC 3.1.1.3)	protein	297	39% helix, 20% strand	Q6WER3

Pockets

11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	241	0.77	0.90	45	empty
2	220	0.76	0.90	44	empty
3	262	0.54	0.77	34	empty
4	158	0.52	0.80	19	empty
5	211	0.49	0.76	29	empty

Interfaces

5 interfaces between chains.

A–B · 994 Å² buried · 21 hydrogen bonds · protein-protein
B–C · 638 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 617 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 64 Å² buried · 0 hydrogen bonds · protein-protein
B–D · 36 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

3NGM · Crystal structure of lipase from Gibberella zeae · 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 Q6WER3
Elsewhere: RCSB PDB 3NGM · PDBe 3NGM · UniProt Q6WER3

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