Research workbench

Bamabcde bound to substrate espp class 1

Analyse Bamabcde bound to substrate espp class 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7TSZ
Type: protein
Length: 1,286 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Outer membrane protein assembly factor bama; Outer membrane protein assembly factor bamb…
EC: 3.4.21.-
UniProt: C3TPJ2, A0A507WQ69, A0A1X3I1M6, W8SZY2, A0A3L5AP29, P0AEX9, Q7BSW5
Pockets: 20 · best druggability 0.80

Structure

electron microscopy · 6 distinct chains · 21% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Outer membrane protein assembly factor bama	protein	595	14% helix, 45% strand	C3TPJ2
B	Outer membrane protein assembly factor bamb	protein	332	0% helix, 42% strand	A0A507WQ69
D	Outer membrane protein assembly factor bamd	protein	213	76% helix, 0% strand	A0A1X3I1M6
C	Outer membrane protein assembly factor bamc	protein	48	15% helix, 0% strand	W8SZY2
E	Outer membrane protein assembly factor bame	protein	88	17% helix, 38% strand	A0A3L5AP29
P	MALTOSE/MALTODEXTRIN-binding periplasmic PROTEIN,SERINE protease espp chimera (EC 3.4.21.-)	protein	10	0% helix, 80% strand	P0AEX9, Q7BSW5

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1138	0.80	0.81	115	empty
2	279	0.74	0.87	54	empty
3	455	0.70	0.81	72	empty
4	380	0.67	0.81	37	empty
5	363	0.62	0.78	47	empty

Interfaces

8 interfaces between chains.

D–C · 1901 Å² buried · 20 hydrogen bonds · protein-protein
A–D · 988 Å² buried · 13 hydrogen bonds · protein-protein
D–E · 789 Å² buried · 9 hydrogen bonds · protein-protein
A–E · 774 Å² buried · 8 hydrogen bonds · protein-protein
A–P · 586 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

7TSZ · BamABCDE bound to substrate EspP class 1 · the same entry in another collection · chain D against D, TM-score 1.00
Q7BSW5 · AlphaFold monomer V2.0 prediction for serine protease espp (Q7BSW5) · a predicted model of the same protein · chain P against A, TM-score 0.49

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 C3TPJ2
Every structure of UniProt A0A507WQ69
Every structure of UniProt A0A1X3I1M6
Every structure of UniProt W8SZY2
Every structure of UniProt A0A3L5AP29
Every structure of UniProt P0AEX9
Every structure of UniProt Q7BSW5
Elsewhere: RCSB PDB 7TSZ · PDBe 7TSZ · UniProt C3TPJ2 · UniProt A0A507WQ69 · UniProt A0A1X3I1M6 · UniProt W8SZY2 · UniProt A0A3L5AP29 · UniProt P0AEX9 · UniProt Q7BSW5

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