MolNFT v1 · #171461 · protein

Cryo-EM structure of the a. baumannii mlabdef complex bound to appnhp

6Z5U · ABC transporter permease: “Cryo-EM structure of the a. baumannii mlabdef complex bound to appnhp”. Electron microscopy, 2 ligands (ANP, MG), 20 pockets (best druggability 0.87). MolNFT v1 #171461 on GenesisL1: 3D structure, binding…

PDB: 6Z5U
Type: protein
Length: 2,334 residues
Chains: 12
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ABC transporter permease; Anti-sigma factor antagonist; Mce family protein; ABC…
UniProt: V5V9F4, V5V9K5, V5V921, A0A4P2WWN2
Ligands: ANP, MG
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 7 distinct chains · 47% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	ABC transporter permease	protein	254	83% helix, 0% strand	V5V9F4
C, D	Anti-sigma factor antagonist	protein	87	41% helix, 2% strand	V5V9K5
E, J	Mce family protein	protein	190	36% helix, 27% strand	V5V921
G	Mce family protein	protein	191	38% helix, 28% strand	V5V921
H	Mce family protein	protein	189	38% helix, 28% strand	V5V921
I, F	Mce family protein	protein	193	40% helix, 27% strand	V5V921
K, L	ABC transporter ATP-binding protein	protein	253	39% helix, 23% strand	A0A4P2WWN2

Ligands and binding sites

ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains B, K, A, L
MG · Magnesium ion · metal · 2 copies · chains K, L

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	735	0.87	0.90	68	empty
2	1083	0.82	0.84	154	empty
3	499	0.79	0.86	43	empty
4	505	0.77	0.84	68	empty
5	371	0.74	0.85	44	empty

Interfaces

27 interfaces between chains.

A–B · 1572 Å² buried · 8 hydrogen bonds · protein-protein
K–L · 1384 Å² buried · 9 hydrogen bonds · protein-protein
A–J · 994 Å² buried · 3 hydrogen bonds · protein-protein
G–H · 989 Å² buried · 6 hydrogen bonds · protein-protein
B–G · 957 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

6Z5U · Cryo-EM structure of the A. baumannii MlaBDEF complex bound to APPNHP · 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 V5V9K5
Every structure of UniProt V5V921
Every structure of UniProt A0A4P2WWN2
Elsewhere: RCSB PDB 6Z5U · PDBe 6Z5U · UniProt V5V9F4 · UniProt V5V9K5 · UniProt V5V921 · UniProt A0A4P2WWN2

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