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T_926 truncate of chlh from thermosynechococcus elongatus at 1.64 a resolution

Analyse T_926 truncate of chlh from thermosynechococcus elongatus at 1.64 a resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6YS9
Type: protein
Length: 1,519 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Magnesium-protoporphyrin methyltransferase
UniProt: Q8DM52
Ligands: K
Pockets: 19 · best druggability 0.72

Structure

x-ray diffraction · 4 distinct chains · 59% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Magnesium-protoporphyrin methyltransferase	protein	381	59% helix, 12% strand	Q8DM52
B	Magnesium-protoporphyrin methyltransferase	protein	380	59% helix, 11% strand	Q8DM52
C	Magnesium-protoporphyrin methyltransferase	protein	378	59% helix, 12% strand	Q8DM52
D	Magnesium-protoporphyrin methyltransferase	protein	380	59% helix, 13% strand	Q8DM52

Ligands and binding sites

K · Potassium ion · metal · 4 copies · chains A, B, C, D

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

Pockets

19 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	965	0.72	0.76	70	empty
2	766	0.71	0.77	90	K
3	991	0.70	0.75	89	empty
4	687	0.65	0.74	52	empty
5	438	0.64	0.78	43	empty

Interfaces

5 interfaces between chains.

A–C · 743 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 702 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 373 Å² buried · 1 hydrogen bond · protein-protein
B–C · 325 Å² buried · 1 hydrogen bond · protein-protein
A–B · 231 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6YS9 · T_926 truncate of ChlH from Thermosynechococcus elongatus at 1.64 A resolution · 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 Q8DM52
Elsewhere: RCSB PDB 6YS9 · PDBe 6YS9 · UniProt Q8DM52

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