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2.9A crystal structure of methyl-isocitrate lyase from burkholderia pseudomallei

Analyse 2.9A crystal structure of methyl-isocitrate lyase from burkholderia pseudomallei in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3EOO
Type: protein
Length: 4,596 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Methylisocitrate lyase
EC: 4.1.3.30
UniProt: B2H5R7
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 7 distinct chains · 52% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Methylisocitrate lyase (EC 4.1.3.30)	protein	290	52% helix, 13% strand	B2H5R7
B, F, K, L, P	Methylisocitrate lyase (EC 4.1.3.30)	protein	286	52% helix, 13% strand	B2H5R7
C, M	Methylisocitrate lyase (EC 4.1.3.30)	protein	287	53% helix, 13% strand	B2H5R7
D, G, N	Methylisocitrate lyase (EC 4.1.3.30)	protein	287	53% helix, 13% strand	B2H5R7
E, H, O	Methylisocitrate lyase (EC 4.1.3.30)	protein	288	52% helix, 13% strand	B2H5R7
I	Methylisocitrate lyase (EC 4.1.3.30)	protein	289	52% helix, 13% strand	B2H5R7
J	Methylisocitrate lyase (EC 4.1.3.30)	protein	288	52% helix, 13% strand	B2H5R7

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	1047	0.87	0.89	127	empty
2	1131	0.87	0.89	119	empty
3	1086	0.87	0.88	125	empty
4	891	0.87	0.89	91	empty
5	1174	0.87	0.88	116	empty

Interfaces

36 interfaces between chains.

M–N · 3781 Å² buried · 35 hydrogen bonds · protein-protein
O–P · 3746 Å² buried · 34 hydrogen bonds · protein-protein
A–B · 3738 Å² buried · 37 hydrogen bonds · protein-protein
K–L · 3738 Å² buried · 38 hydrogen bonds · protein-protein
G–H · 3731 Å² buried · 32 hydrogen bonds · protein-protein

Compared structures

3EOO · 2.9A crystal structure of methyl-isocitrate lyase from Burkholderia pseudomallei · 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 B2H5R7
Elsewhere: RCSB PDB 3EOO · PDBe 3EOO · UniProt B2H5R7

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