Research workbench

Bamabcde bound to substrate espp class 3

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

PDB: 7TT2
Type: protein
Length: 1,328 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Outer membrane protein assembly factor bamd; Outer membrane protein assembly factor bamc…
EC: 3.4.21.-
UniProt: A0A1X3I1M6, W8SZY2, A0A3L5AP29, A0A507WQ69, C3TPJ2, Q7BSW5
Pockets: 19 · best druggability 0.80

Structure

electron microscopy · 6 distinct chains · 20% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D	Outer membrane protein assembly factor bamd	protein	213	76% helix, 0% strand	A0A1X3I1M6
C	Outer membrane protein assembly factor bamc	protein	48	13% helix, 0% strand	W8SZY2
E	Outer membrane protein assembly factor bame	protein	89	17% helix, 37% strand	A0A3L5AP29
B	Outer membrane protein assembly factor bamb	protein	350	1% helix, 49% strand	A0A507WQ69
A	Outer membrane protein assembly factor bama	protein	610	13% helix, 45% strand	C3TPJ2
P	MALTOSE/MALTODEXTRIN-binding periplasmic PROTEIN,SERINE protease espp chimera (EC 3.4.21.-)	protein	18	0% helix, 50% strand	Q7BSW5

Pockets

19 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	1146	0.80	0.81	117	empty
2	640	0.74	0.81	83	empty
3	61	0.67	0.95	23	empty
4	426	0.66	0.79	61	empty
5	291	0.59	0.78	37	empty

Interfaces

8 interfaces between chains.

D–C · 1748 Å² buried · 18 hydrogen bonds · protein-protein
D–A · 1019 Å² buried · 13 hydrogen bonds · protein-protein
B–A · 913 Å² buried · 14 hydrogen bonds · protein-protein
E–A · 823 Å² buried · 8 hydrogen bonds · protein-protein
D–E · 787 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

7TT2 · BamABCDE bound to substrate EspP class 3 · the same entry in another collection · chain E against E, 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 0.36

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 A0A1X3I1M6
Every structure of UniProt W8SZY2
Every structure of UniProt A0A3L5AP29
Every structure of UniProt A0A507WQ69
Every structure of UniProt C3TPJ2
Every structure of UniProt Q7BSW5
Elsewhere: RCSB PDB 7TT2 · PDBe 7TT2 · UniProt A0A1X3I1M6 · UniProt W8SZY2 · UniProt A0A3L5AP29 · UniProt A0A507WQ69 · UniProt C3TPJ2 · UniProt Q7BSW5

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