MolNFT v1 · #134572 · protein

Crystal structure of cdi complex from cupriavidus taiwanensis lmg 19424

5T87 · Cdii immunity protein: “Crystal structure of cdi complex from cupriavidus taiwanensis lmg 19424”. X-ray diffraction, 7 pockets (best druggability 0.73). MolNFT v1 #134572 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5T87
Type: protein
Length: 745 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cdii immunity protein; Cdia toxin
UniProt: B3R1C2, B3R1C1
Pockets: 7 · best druggability 0.73

Structure

x-ray diffraction · 7 distinct chains · 49% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cdii immunity protein	protein	114	72% helix, 2% strand	B3R1C2
B	Cdii immunity protein	protein	113	69% helix, 2% strand	B3R1C2
C, D	Cdii immunity protein	protein	115	68% helix, 2% strand	B3R1C2
E	Cdia toxin	protein	69	25% helix, 38% strand	B3R1C1
F	Cdia toxin	protein	74	24% helix, 32% strand	B3R1C1
G	Cdia toxin	protein	75	25% helix, 37% strand	B3R1C1
H	Cdia toxin	protein	70	26% helix, 30% strand	B3R1C1

Pockets

7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	717	0.73	0.79	71	empty
2	763	0.69	0.76	84	empty
3	61	0.38	0.80	20	empty
4	66	0.38	0.79	20	empty
5	51	0.37	0.81	19	empty

Interfaces

11 interfaces between chains.

B–F · 1192 Å² buried · 20 hydrogen bonds · protein-protein
C–G · 1169 Å² buried · 20 hydrogen bonds · protein-protein
A–E · 1162 Å² buried · 21 hydrogen bonds · protein-protein
D–H · 1149 Å² buried · 19 hydrogen bonds · protein-protein
B–C · 461 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 modified (engineered).

Compared structures

5T87 · Crystal structure of CDI complex from Cupriavidus taiwanensis LMG 19424 · 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 B3R1C2
Every structure of UniProt B3R1C1
Elsewhere: RCSB PDB 5T87 · PDBe 5T87 · UniProt B3R1C2 · UniProt B3R1C1

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.