MolNFT v1 · #148987 · protein

Imisx-ep of se-lspa

6FMS · Lipoprotein signal peptidase: “Imisx-ep of se-lspa”. X-ray diffraction, 1 ligand (5BV), 5 pockets (best druggability 0.60). MolNFT v1 #148987 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6FMS
Type: protein
Length: 628 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lipoprotein signal peptidase; Globomycin
EC: 3.4.23.36
UniProt: Q9HVM5
Ligands: 5BV
Pockets: 5 · best druggability 0.60

Structure

x-ray diffraction · 3 distinct chains · 56% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Lipoprotein signal peptidase (EC 3.4.23.36)	protein	157	59% helix, 13% strand	Q9HVM5
C, D	Lipoprotein signal peptidase (EC 3.4.23.36)	protein	149	54% helix, 17% strand	Q9HVM5
E, F, G, H	Globomycin	protein	4	0% helix, 0% strand	—

Ligands and binding sites

5BV · (2R,3R)-3-(glycyloxy)-2-methylnonanoic acid · ligand · 4 copies · chains A, E, B, F, C, D, G, H
OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 22 copies · chains A, B, F, C, G, D, E, H

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	443	0.60	0.75	44	empty
2	205	0.58	0.80	40	empty
3	329	0.57	0.76	50	empty
4	131	0.40	0.75	21	empty
5	65	0.28	0.73	16	empty

Interfaces

8 interfaces between chains.

C–G · 436 Å² buried · 10 hydrogen bonds · protein-protein
A–E · 420 Å² buried · 7 hydrogen bonds · protein-protein
B–F · 419 Å² buried · 6 hydrogen bonds · protein-protein
D–H · 409 Å² buried · 10 hydrogen bonds · protein-protein
B–D · 333 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 28 modified, 8 covalent (engineered, nonstandard, covalent ligand).

Compared structures

6FMS · IMISX-EP of Se-LspA · the same entry in another collection · chain H against H, TM-score 1.00
Q9HVM5 · AlphaFold monomer V2.0 prediction for lipoprotein signal peptidase (Q9HVM5) · a predicted model of the same protein · chain C against A, TM-score 0.95

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 Q9HVM5
Elsewhere: RCSB PDB 6FMS · PDBe 6FMS · UniProt Q9HVM5

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