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Crystal structure of the oxalate bound malyl-CoA lyase from roseiflexus castenholzii

Analyse Crystal structure of the oxalate bound 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: 6KKH
Type: protein
Length: 4,035 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HPCH/HPAI aldolase
UniProt: A7NHT0
Ligands: OXL, MG
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 11 distinct chains · 44% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HPCH/HPAI aldolase	protein	329	44% helix, 14% strand	A7NHT0
B	HPCH/HPAI aldolase	protein	345	43% helix, 15% strand	A7NHT0
C	HPCH/HPAI aldolase	protein	343	44% helix, 15% strand	A7NHT0
D	HPCH/HPAI aldolase	protein	328	45% helix, 15% strand	A7NHT0
E	HPCH/HPAI aldolase	protein	347	44% helix, 14% strand	A7NHT0
F, L	HPCH/HPAI aldolase	protein	342	46% helix, 14% strand	A7NHT0
G	HPCH/HPAI aldolase	protein	325	43% helix, 14% strand	A7NHT0
H	HPCH/HPAI aldolase	protein	316	43% helix, 14% strand	A7NHT0
I	HPCH/HPAI aldolase	protein	345	43% helix, 15% strand	A7NHT0
J	HPCH/HPAI aldolase	protein	346	45% helix, 15% strand	A7NHT0
K	HPCH/HPAI aldolase	protein	327	40% helix, 15% strand	A7NHT0

Ligands and binding sites

OXL · Oxalate ion · ligand · 4 copies · chains B, C, A, F, H, I, G, L
MG · Magnesium ion · metal · 2 copies · chains A, F, H, I
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains A, E, F, B, C, D, G, K, L, H, I, J

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	1093	0.87	0.88	103	empty
2	1095	0.86	0.87	112	empty
3	1123	0.86	0.87	91	empty
4	1199	0.85	0.86	102	empty
5	1141	0.85	0.86	85	empty

Interfaces

25 interfaces between chains.

A–F · 2147 Å² buried · 24 hydrogen bonds · protein-protein
H–I · 2120 Å² buried · 24 hydrogen bonds · protein-protein
B–C · 1949 Å² buried · 20 hydrogen bonds · protein-protein
G–L · 1880 Å² buried · 17 hydrogen bonds · protein-protein
K–L · 1694 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

6KKH · Crystal structure of the oxalate bound 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 6KKH · PDBe 6KKH · UniProt A7NHT0

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