MolNFT v1 · #139691 · protein

Crystal structure of the icms-icmw-dotl complex of the legionella type ivb secretion system

5XNB: “Crystal structure of the icms-icmw-dotl complex of the legionella type ivb secretion system”. X-ray diffraction, 17 pockets (best druggability 0.56). MolNFT v1 #139691 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5XNB
Type: protein
Length: 2,196 residues
Chains: 18
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dotl; Icms protein; Icmw
UniProt: O54524, O54636, Q48800
Pockets: 17 · best druggability 0.56

Structure

x-ray diffraction · 10 distinct chains · 57% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dotl	protein	104	52% helix, 2% strand	O54524
B, E, Q	Icms protein	protein	114	46% helix, 17% strand	O54636
C, F, L, O	Icmw	protein	149	69% helix, 0% strand	Q48800
D	Dotl	protein	107	53% helix, 2% strand	O54524
G	Dotl	protein	102	53% helix, 2% strand	O54524
H, K, N	Icms protein	protein	115	50% helix, 17% strand	O54636
I, R	Icmw	protein	148	70% helix, 0% strand	Q48800
J	Dotl	protein	101	54% helix, 2% strand	O54524
M	Dotl	protein	103	54% helix, 0% strand	O54524
P	Dotl	protein	100	55% helix, 0% strand	O54524

Ligands and binding sites

BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · 5 copies · chains C, F, I, L, R

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

Pockets

17 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	113	0.56	0.84	28	empty
2	93	0.56	0.86	25	empty
3	77	0.55	0.86	18	empty
4	91	0.53	0.84	27	empty
5	176	0.51	0.78	38	empty

Interfaces

25 interfaces between chains.

M–O · 2851 Å² buried · 26 hydrogen bonds · protein-protein
J–L · 2818 Å² buried · 22 hydrogen bonds · protein-protein
G–I · 2804 Å² buried · 15 hydrogen bonds · protein-protein
A–C · 2794 Å² buried · 20 hydrogen bonds · protein-protein
P–R · 2792 Å² buried · 25 hydrogen bonds · protein-protein

Compared structures

5XNB · Crystal structure of the IcmS-IcmW-DotL complex of the Legionella type IVb secretion… · 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 O54524
Every structure of UniProt O54636
Every structure of UniProt Q48800
Elsewhere: RCSB PDB 5XNB · PDBe 5XNB · UniProt O54524 · UniProt O54636 · UniProt Q48800

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