MolNFT v1 · #83978 · protein

Structure of the periplasmic domain of doti (crystal form II)

3WZ5: “Structure of the periplasmic domain of doti (crystal form II)”. X-ray diffraction, 6 pockets (best druggability 0.68). MolNFT v1 #83978 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3WZ5
Type: protein
Length: 541 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Doti
UniProt: O54626
Pockets: 6 · best druggability 0.68

Structure

x-ray diffraction · 2 distinct chains · 32% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	Doti	protein	135	31% helix, 38% strand	O54626
C	Doti	protein	136	34% helix, 41% strand	O54626

Pockets

6 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	963	0.68	0.74	83	empty
2	223	0.66	0.84	30	empty
3	174	0.64	0.84	25	empty
4	138	0.62	0.85	22	empty
5	128	0.61	0.85	23	empty

Interfaces

5 interfaces between chains.

C–D · 716 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 698 Å² buried · 13 hydrogen bonds · protein-protein
A–D · 461 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 436 Å² buried · 1 hydrogen bond · protein-protein
B–D · 35 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 modified (engineered).

Compared structures

3WZ5 · Structure of the periplasmic domain of DotI (crystal form II) · 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 O54626
Elsewhere: RCSB PDB 3WZ5 · PDBe 3WZ5 · UniProt O54626

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