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Crystal structure of 2,3-dimethylmalate lyase, a pep MUTASE/ISOCITRATE lyase superfamily member, triclinic crystal form

Analyse Crystal structure of 2,3-dimethylmalate lyase, a pep MUTASE/ISOCITRATE lyase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3FA4
Type: protein
Length: 3,407 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 2,3-dimethylmalate lyase
EC: 4.1.3.32
UniProt: Q2L887
Ligands: MG
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 11 distinct chains · 50% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, G	2,3-dimethylmalate lyase (EC 4.1.3.32)	protein	284	49% helix, 13% strand	Q2L887
B	2,3-dimethylmalate lyase (EC 4.1.3.32)	protein	288	49% helix, 13% strand	Q2L887
C	2,3-dimethylmalate lyase (EC 4.1.3.32)	protein	284	50% helix, 13% strand	Q2L887
D	2,3-dimethylmalate lyase (EC 4.1.3.32)	protein	284	50% helix, 13% strand	Q2L887
E	2,3-dimethylmalate lyase (EC 4.1.3.32)	protein	286	50% helix, 13% strand	Q2L887
F	2,3-dimethylmalate lyase (EC 4.1.3.32)	protein	285	49% helix, 13% strand	Q2L887
H	2,3-dimethylmalate lyase (EC 4.1.3.32)	protein	282	50% helix, 13% strand	Q2L887
I	2,3-dimethylmalate lyase (EC 4.1.3.32)	protein	282	50% helix, 13% strand	Q2L887
J	2,3-dimethylmalate lyase (EC 4.1.3.32)	protein	280	51% helix, 13% strand	Q2L887
K	2,3-dimethylmalate lyase (EC 4.1.3.32)	protein	280	51% helix, 13% strand	Q2L887
L	2,3-dimethylmalate lyase (EC 4.1.3.32)	protein	288	49% helix, 13% strand	Q2L887

Ligands and binding sites

MG · Magnesium ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L

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	1200	0.88	0.90	206	MG
2	1162	0.88	0.89	153	MG
3	1070	0.83	0.84	129	MG
4	221	0.78	0.92	57	MG
5	1074	0.76	0.78	117	MG

Interfaces

23 interfaces between chains.

K–L · 3153 Å² buried · 26 hydrogen bonds · protein-protein
C–D · 3031 Å² buried · 26 hydrogen bonds · protein-protein
E–F · 2995 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 2981 Å² buried · 23 hydrogen bonds · protein-protein
G–H · 2960 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

3FA4 · Crystal structure of 2,3-dimethylmalate lyase, a PEP mutase/isocitrate lyase superfamily… · 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 Q2L887
Elsewhere: RCSB PDB 3FA4 · PDBe 3FA4 · UniProt Q2L887

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