MolNFT v1 · #141675 · protein

Structure of the EXBB/EXBD hexameric complex

5ZFP · Biopolymer transport protein exbb: “Structure of the EXBB/EXBD hexameric complex”. X-ray diffraction, 20 pockets (best druggability 0.76). MolNFT v1 #141675 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5ZFP
Type: protein
Length: 2,633 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Biopolymer transport protein exbb
UniProt: P0ABU7
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 8 distinct chains · 87% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, G	Biopolymer transport protein exbb	protein	225	87% helix, 0% strand	P0ABU7
B, L	Biopolymer transport protein exbb	protein	215	87% helix, 0% strand	P0ABU7
C, I	Biopolymer transport protein exbb	protein	223	87% helix, 0% strand	P0ABU7
D	Biopolymer transport protein exbb	protein	215	87% helix, 0% strand	P0ABU7
E	Biopolymer transport protein exbb	protein	222	88% helix, 0% strand	P0ABU7
F, H	Biopolymer transport protein exbb	protein	216	87% helix, 0% strand	P0ABU7
J	Biopolymer transport protein exbb	protein	214	86% helix, 0% strand	P0ABU7
K	Biopolymer transport protein exbb	protein	224	87% helix, 0% strand	P0ABU7

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	665	0.76	0.81	79	empty
2	519	0.73	0.81	48	empty
3	346	0.71	0.83	38	empty
4	780	0.69	0.76	88	empty
5	794	0.69	0.76	81	empty

Interfaces

17 interfaces between chains.

I–J · 1604 Å² buried · 15 hydrogen bonds · protein-protein
G–L · 1600 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 1587 Å² buried · 11 hydrogen bonds · protein-protein
H–I · 1573 Å² buried · 11 hydrogen bonds · protein-protein
A–F · 1569 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

5ZFP · Structure of the ExbB/ExbD hexameric complex · the same entry in another collection · chain L against L, 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 P0ABU7
Elsewhere: RCSB PDB 5ZFP · PDBe 5ZFP · UniProt P0ABU7

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