Research workbench

Bacterial ABC transporter involved in B12 uptake

Analyse Bacterial ABC transporter involved in B12 uptake in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1L7V
Type: protein
Length: 1,110 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vitamin B12 transport system permease protein btuc; Vitamin B12 transport ATP-binding…
EC: 3.6.3.33
UniProt: P06609, P06611
Ligands: V4O
Pockets: 14 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 61% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Vitamin B12 transport system permease protein btuc	protein	324	77% helix, 1% strand	P06609
C, D	Vitamin B12 transport ATP-binding protein btud (EC 3.6.3.33)	protein	231	39% helix, 19% strand	P06611

Ligands and binding sites

V4O · Cyclo-tetrametavanadate · ligand · 2 copies · chains C, D

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

Pockets

14 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	1137	0.83	0.84	107	empty
2	810	0.75	0.80	98	V4O
3	873	0.73	0.78	86	empty
4	836	0.73	0.78	88	empty
5	310	0.60	0.78	46	empty

Interfaces

4 interfaces between chains.

A–B · 1332 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 1075 Å² buried · 12 hydrogen bonds · protein-protein
B–D · 1066 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 566 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 36 modified (engineered).

Compared structures

1L7V · Bacterial ABC Transporter Involved in B12 Uptake · the same entry in another collection · chain A against A, TM-score 1.00
P06611 · AlphaFold monomer V2.0 prediction for vitamin B12 import ATP-binding protein btud (P06611) · a predicted model of the same protein · chain D against A, TM-score 0.99
P06609 · AlphaFold monomer V2.0 prediction for vitamin B12 import system permease protein btuc… · a predicted model of the same protein · chain A against A, TM-score 0.93

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 P06609
Every structure of UniProt P06611
Elsewhere: RCSB PDB 1L7V · PDBe 1L7V · UniProt P06609 · UniProt P06611

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