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Crystal structure of the suscd complex BT2261-2264 from bacteroides thetaiotaomicron

Analyse Crystal structure of the suscd complex BT2261-2264 from bacteroides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5FQ6
Type: protein
Length: 6,325 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative lipoprotein; SUSC/RAGA family tonb-linked outer membrane protein…
UniProt: Q8A5H6, Q8A5H5, Q8A5H8
Ligands: KR0, NA, CA
Pockets: 20 · best druggability 0.89

Structure

x-ray diffraction · 7 distinct chains · 15% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, H, L	Putative lipoprotein	protein	480	52% helix, 5% strand	Q8A5H6
B	SUSC/RAGA family tonb-linked outer membrane protein	protein	941	11% helix, 50% strand	Q8A5H5
D	SUSC/RAGA family tonb-linked outer membrane protein	protein	945	10% helix, 50% strand	Q8A5H5
E, F, J, N	Uncharacterized protein	protein	146	4% helix, 50% strand	Q8A5H8
G, K, O, P	BT_2261	protein	10	0% helix, 0% strand	—
I	SUSC/RAGA family tonb-linked outer membrane protein	protein	947	11% helix, 50% strand	Q8A5H5
M	SUSC/RAGA family tonb-linked outer membrane protein	protein	948	12% helix, 50% strand	Q8A5H5

Ligands and binding sites

KR0 · 3-decanoyloxypropyl decanoate · ligand · 4 copies · chains A, B, I, C, D, M, H, L
NA · Sodium ion · metal · 4 copies · chains A, B, C, D, H, I, L, M
CA · Calcium ion · metal · 4 copies · chains B, D, I, M

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

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	991	0.89	0.91	122	empty
2	1011	0.89	0.90	134	empty
3	924	0.88	0.91	108	empty
4	918	0.88	0.90	111	empty
5	194	0.82	0.97	41	empty

Interfaces

28 interfaces between chains.

L–M · 4090 Å² buried · 61 hydrogen bonds · protein-protein
H–I · 4086 Å² buried · 48 hydrogen bonds · protein-protein
C–D · 4076 Å² buried · 49 hydrogen bonds · protein-protein
A–B · 4073 Å² buried · 57 hydrogen bonds · protein-protein
D–M · 2953 Å² buried · 42 hydrogen bonds · protein-protein

Compared structures

5FQ6 · Crystal structure of the SusCD complex BT2261-2264 from Bacteroides thetaiotaomicron · the same entry in another collection · chain A against A, TM-score 1.00

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 Q8A5H6
Every structure of UniProt Q8A5H5
Every structure of UniProt Q8A5H8
Elsewhere: RCSB PDB 5FQ6 · PDBe 5FQ6 · UniProt Q8A5H6 · UniProt Q8A5H5 · UniProt Q8A5H8

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