Research workbench

Lateral-open conformation of the wild-type bam complex (bamabcde) bound to a bactericidal Fab fragment

Analyse Lateral-open conformation of the wild-type bam complex (bamabcde) bound to a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7ND0
Type: protein
Length: 1,960 residues
Chains: 7
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Outer membrane protein assembly factor bama; Outer membrane protein assembly factor bamb…
UniProt: P0A940, P77774, P0A903, P0AC02, P0A937
Pockets: 20 · best druggability 0.82

Structure

electron microscopy · 7 distinct chains · 17% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Outer membrane protein assembly factor bama	protein	787	17% helix, 36% strand	P0A940
B	Outer membrane protein assembly factor bamb	protein	371	0% helix, 41% strand	P77774
C	Outer membrane protein assembly factor bamc	protein	61	11% helix, 0% strand	P0A903
D	Outer membrane protein assembly factor bamd	protein	218	75% helix, 0% strand	P0AC02
E	Outer membrane protein assembly factor bame	protein	87	13% helix, 28% strand	P0A937
H	FAB1 heavy chain	protein	221	5% helix, 50% strand	—
L	FAB1 light chain	protein	215	3% helix, 48% strand	—

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	690	0.82	0.86	96	empty
2	332	0.78	0.89	55	empty
3	215	0.77	0.91	52	empty
4	142	0.76	0.93	32	empty
5	159	0.75	0.93	31	empty

Interfaces

9 interfaces between chains.

C–D · 1992 Å² buried · 22 hydrogen bonds · protein-protein
H–L · 1722 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 1302 Å² buried · 19 hydrogen bonds · protein-protein
A–D · 1132 Å² buried · 20 hydrogen bonds · protein-protein
A–E · 719 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

7ND0 · lateral-open conformation of the wild-type BAM complex (BamABCDE) bound to a bactericidal… · the same entry in another collection · chain L against L, TM-score 1.00
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 0.94
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 0.93
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 0.85
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 0.69
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 0.56

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
Elsewhere: RCSB PDB 7ND0 · PDBe 7ND0 · UniProt P0A940 · UniProt P77774 · UniProt P0A903 · UniProt P0AC02 · UniProt P0A937

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