Research workbench

Structure of the BAM complex

Analyse Structure of the BAM complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6LYQ
Type: protein
Length: 1,508 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.19
Source: Escherichia coli K-12
Molecule: Outer membrane protein assembly factor BamA; Outer membrane protein assembly factor BamB…
UniProt: P0A940, P77774, P0A903, P0AC02, P0A937, P0A921
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · resolution 3.19 · 6 distinct chains · 19% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Outer membrane protein assembly factor BamA	protein	787	15% helix, 42% strand	P0A940
B	Outer membrane protein assembly factor BamB	protein	356	0% helix, 46% strand	P77774
C	Outer membrane protein assembly factor BamC	protein	56	13% helix, 0% strand	P0A903
D	Outer membrane protein assembly factor BamD	protein	208	72% helix, 0% strand	P0AC02
E	Outer membrane protein assembly factor BamE	protein	88	14% helix, 38% strand	P0A937
O	Peptide from Phospholipase A1	protein	13	0% helix, 62% strand	P0A921

Pockets

20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	713	0.79	0.83	83	empty
2	120	0.78	0.97	34	empty
3	863	0.73	0.78	86	empty
4	287	0.57	0.77	44	empty
5	165	0.57	0.81	25	empty

Interfaces

7 interfaces between chains.

C–D · 1999 Å² buried · 13 hydrogen bonds · protein-protein
A–D · 1635 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 1104 Å² buried · 16 hydrogen bonds · protein-protein
A–E · 930 Å² buried · 10 hydrogen bonds · protein-protein
A–O · 775 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

6LYQ · Structure of the bam complex · the same entry in another collection · chain O against O, TM-score 1.00
P77774 · AlphaFold monomer V2.0 prediction for outer membrane protein assembly factor bamb (P77774) · a predicted model of the same protein · chain B against A, TM-score 0.98
P0A940 · AlphaFold monomer V2.0 prediction for outer membrane protein assembly factor bama (P0A940) · a predicted model of the same protein · chain A against A, TM-score 0.97
P0AC02 · AlphaFold monomer V2.0 prediction for outer membrane protein assembly factor bamd (P0AC02) · a predicted model of the same protein · chain D against A, TM-score 0.95
P0A937 · AlphaFold monomer V2.0 prediction for outer membrane protein assembly factor bame (P0A937) · a predicted model of the same protein · chain E against A, TM-score 0.90
P0A903 · AlphaFold monomer V2.0 prediction for outer membrane protein assembly factor bamc (P0A903) · a predicted model of the same protein · chain C against A, TM-score 0.71
P0A921 · AlphaFold monomer V2.0 prediction for phospholipase A1 (P0A921) · a predicted model of the same protein · chain O against A, TM-score 0.20

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 P0A940
Every structure of UniProt P77774
Every structure of UniProt P0A903
Every structure of UniProt P0AC02
Every structure of UniProt P0A937
Every structure of UniProt P0A921
Elsewhere: RCSB PDB 6LYQ · PDBe 6LYQ · UniProt P0A940 · UniProt P77774 · UniProt P0A903 · UniProt P0AC02 · UniProt P0A937 · UniProt P0A921

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