MolNFT v1 · #154632 · protein

Lipase (open form)

6KHM · Hydrolase, ALPHA/BETA domain protein: “Lipase (open form)”. X-ray diffraction, 5 ligands (DKF, DKL, DK6), 20 pockets (best druggability 0.83). MolNFT v1 #154632 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6KHM
Type: protein
Length: 8,053 residues
Chains: 26
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hydrolase, ALPHA/BETA domain protein
UniProt: E6DAE5
Ligands: DKF, DKL, DK6, DKO, DK9
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 5 distinct chains · 43% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, G, J, N, O, P, S, U, W	Hydrolase, ALPHA/BETA domain protein	protein	310	44% helix, 16% strand	E6DAE5
B, C, H, M, R, T, V, X, Y, Z	Hydrolase, ALPHA/BETA domain protein	protein	309	43% helix, 17% strand	E6DAE5
D, F	Hydrolase, ALPHA/BETA domain protein	protein	308	43% helix, 17% strand	E6DAE5
E, I, Q	Hydrolase, ALPHA/BETA domain protein	protein	311	42% helix, 16% strand	E6DAE5
K, L	Hydrolase, ALPHA/BETA domain protein	protein	312	42% helix, 17% strand	E6DAE5

Ligands and binding sites

DKF · hexane-1,1-diol · ligand · 11 copies · chains E, G, I, J, K, L, M, U, V, Y, W
DKL · heptane-1,1-diol · ligand · 5 copies · chains A, C, Q, T, X
DK6 · propane-1,1-diol · ligand · 4 copies · chains D, H, S, Z
DKO · octane-1,1-diol · ligand · 3 copies · chains B, N, R
DK9 · pentane-1,1-diol · ligand · 3 copies · chains F, O, P

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	467	0.83	0.90	64	empty
2	430	0.83	0.91	63	empty
3	452	0.82	0.90	65	empty
4	772	0.80	0.84	102	empty
5	261	0.80	0.91	36	empty

Interfaces

38 interfaces between chains.

K–L · 1225 Å² buried · 17 hydrogen bonds · protein-protein
C–D · 1222 Å² buried · 18 hydrogen bonds · protein-protein
S–T · 1220 Å² buried · 18 hydrogen bonds · protein-protein
I–J · 1216 Å² buried · 17 hydrogen bonds · protein-protein
E–F · 1215 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 17 covalent (covalent ligand).

Compared structures

6KHM · Lipase (Open form) · the same entry in another collection · chain B against B, 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 E6DAE5
Elsewhere: RCSB PDB 6KHM · PDBe 6KHM · UniProt E6DAE5

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