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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: 5FQ8
Type: protein
Length: 3,367 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative lipoprotein; Outer membrane protein OMP121; Uncharacterized protein; BT_2262…
UniProt: Q8A5H6, Q8A5H5, Q8A5H8, Q8A5H7
Ligands: KR0, MG, CA
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 9 distinct chains · 21% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative lipoprotein	protein	480	51% helix, 5% strand	Q8A5H6
B	Outer membrane protein OMP121	protein	945	11% helix, 50% strand	Q8A5H5
C	Putative lipoprotein	protein	479	50% helix, 5% strand	Q8A5H6
D	Outer membrane protein OMP121	protein	941	11% helix, 50% strand	Q8A5H5
E	Uncharacterized protein	protein	145	4% helix, 49% strand	Q8A5H8
F	Uncharacterized protein	protein	146	4% helix, 49% strand	Q8A5H8
G	BT_2262 (uncharacterised lipoprotein)	protein	212	3% helix, 47% strand	Q8A5H7
P	Uncharacterised protein, bound peptide	protein	10	0% helix, 0% strand	—
Q	Uncharacterised protein, bound peptide	protein	9	0% helix, 11% strand	—

Ligands and binding sites

KR0 · 3-decanoyloxypropyl decanoate · ligand · 2 copies · chains A, B, D, C
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
CA · Calcium ion · metal · 4 copies · chains B, F, D, E
C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 4 copies · chains B, D

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	1160	0.88	0.89	126	empty
2	817	0.87	0.90	95	empty
3	219	0.82	0.96	43	empty
4	206	0.82	0.96	42	empty
5	657	0.80	0.85	82	empty

Interfaces

15 interfaces between chains.

A–B · 4088 Å² buried · 55 hydrogen bonds · protein-protein
C–D · 4020 Å² buried · 50 hydrogen bonds · protein-protein
B–D · 3005 Å² buried · 43 hydrogen bonds · protein-protein
B–F · 1173 Å² buried · 21 hydrogen bonds · protein-protein
D–E · 1154 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 covalent (covalent ligand).

Compared structures

5FQ8 · 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
Every structure of UniProt Q8A5H7
Elsewhere: RCSB PDB 5FQ8 · PDBe 5FQ8 · UniProt Q8A5H6 · UniProt Q8A5H5 · UniProt Q8A5H8 · UniProt Q8A5H7

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