Research workbench

Acinetobacter mlafedb complex in ADP-vanadate trapped vclose conformation

Analyse Acinetobacter mlafedb complex in ADP-vanadate trapped vclose conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7D0A
Type: protein
Length: 2,374 residues
Chains: 12
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Intermembrane phospholipid transport system permease protein mlae; ABC transporter…
UniProt: V5V9F4, A0A086HZU3, V5V9K5, V5V921
Ligands: ADP, VO4
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 4 distinct chains · 44% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Intermembrane phospholipid transport system permease protein mlae	protein	256	82% helix, 0% strand	V5V9F4
B, E	ABC transporter ATP-binding protein	protein	263	28% helix, 13% strand	A0A086HZU3
C, F	Anti-sigma factor antagonist	protein	95	25% helix, 4% strand	V5V9K5
G, H, I, J, K, L	Mce family protein	protein	191	24% helix, 23% strand	V5V921

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains B, E
VO4 · Vanadate ion · ion · 2 copies · chains B, E

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	924	0.88	0.89	127	empty
2	829	0.82	0.84	98	ADP, VO4
3	506	0.80	0.87	71	empty
4	185	0.78	0.93	36	empty
5	271	0.77	0.89	42	empty

Interfaces

28 interfaces between chains.

B–E · 2329 Å² buried · 24 hydrogen bonds · protein-protein
A–D · 1795 Å² buried · 10 hydrogen bonds · protein-protein
G–L · 1199 Å² buried · 3 hydrogen bonds · protein-protein
I–J · 1098 Å² buried · 4 hydrogen bonds · protein-protein
D–J · 1094 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

7D0A · Acinetobacter MlaFEDB complex in ADP-vanadate trapped Vclose conformation · 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 V5V9F4
Every structure of UniProt A0A086HZU3
Every structure of UniProt V5V9K5
Every structure of UniProt V5V921
Elsewhere: RCSB PDB 7D0A · PDBe 7D0A · UniProt V5V9F4 · UniProt A0A086HZU3 · UniProt V5V9K5 · UniProt V5V921

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