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Crystal structure of a THY1-complementing protein (TM0449) from thermotoga maritima at 2.25 a resolution

Analyse Crystal structure of a THY1-complementing protein (TM0449) from thermotoga… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1KQ4
Type: protein
Length: 838 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hypothetical protein TM0449
UniProt: Q9WYT0
Ligands: FAD
Pockets: 7 · best druggability 0.85

Structure

x-ray diffraction · 4 distinct chains · 52% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hypothetical protein TM0449	protein	203	53% helix, 19% strand	Q9WYT0
B	Hypothetical protein TM0449	protein	211	52% helix, 18% strand	Q9WYT0
C	Hypothetical protein TM0449	protein	214	52% helix, 18% strand	Q9WYT0
D	Hypothetical protein TM0449	protein	210	51% helix, 18% strand	Q9WYT0

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, C, D, B

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

Pockets

7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	577	0.85	0.90	56	FAD
2	259	0.72	0.86	36	FAD
3	142	0.70	0.90	26	empty
4	76	0.62	0.90	18	empty
5	127	0.61	0.85	22	empty

Interfaces

6 interfaces between chains.

B–C · 2191 Å² buried · 28 hydrogen bonds · protein-protein
A–D · 2114 Å² buried · 25 hydrogen bonds · protein-protein
C–D · 1328 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 1167 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 233 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 modified (engineered).

Compared structures

1KQ4 · Crystal structure of a THY1-complementing protein (TM0449) from thermotoga maritima at… · 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 Q9WYT0
Elsewhere: RCSB PDB 1KQ4 · PDBe 1KQ4 · UniProt Q9WYT0

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