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Crystal structure of the tri-functional malyl-CoA lyase from roseiflexus castenholzii

Analyse Crystal structure of the tri-functional malyl-CoA lyase from roseiflexus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6KIN
Type: protein
Length: 2,062 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HPCH/HPAI aldolase
UniProt: A7NHT0
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 5 distinct chains · 45% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	HPCH/HPAI aldolase	protein	344	44% helix, 15% strand	A7NHT0
C	HPCH/HPAI aldolase	protein	341	46% helix, 15% strand	A7NHT0
D	HPCH/HPAI aldolase	protein	345	46% helix, 15% strand	A7NHT0
E	HPCH/HPAI aldolase	protein	346	45% helix, 15% strand	A7NHT0
F	HPCH/HPAI aldolase	protein	342	45% helix, 15% strand	A7NHT0

Ligands and binding sites

TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B, E, C, D, F

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	1134	0.86	0.87	97	empty
2	1166	0.85	0.86	93	empty
3	1172	0.84	0.85	90	empty
4	1199	0.83	0.84	83	empty
5	632	0.76	0.82	83	empty

Interfaces

12 interfaces between chains.

C–F · 2129 Å² buried · 27 hydrogen bonds · protein-protein
B–E · 1837 Å² buried · 20 hydrogen bonds · protein-protein
C–D · 1668 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 1644 Å² buried · 19 hydrogen bonds · protein-protein
A–E · 1594 Å² buried · 24 hydrogen bonds · protein-protein

Compared structures

6KIN · Crystal structure of the tri-functional malyl-CoA lyase from Roseiflexus castenholzii · 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 A7NHT0
Elsewhere: RCSB PDB 6KIN · PDBe 6KIN · UniProt A7NHT0

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