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Yeast isocitrate dehydrogenase with citrate and AMP bound in the regulatory subunits

Analyse Yeast isocitrate dehydrogenase with citrate and AMP bound in the regulatory… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3BLW
Type: protein
Length: 5,443 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Isocitrate dehydrogenase [NAD] subunit 1; Isocitrate dehydrogenase [NAD] subunit 2
EC: 1.1.1.41
UniProt: P28834, P28241
Ligands: AMP
Pockets: 20 · best druggability 0.75

Structure

x-ray diffraction · 7 distinct chains · 41% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, G, I	Isocitrate dehydrogenase [NAD] subunit 1 (EC 1.1.1.41)	protein	329	42% helix, 22% strand	P28834
B, D, F, J, N, P	Isocitrate dehydrogenase [NAD] subunit 2 (EC 1.1.1.41)	protein	347	39% helix, 20% strand	P28241
C, E	Isocitrate dehydrogenase [NAD] subunit 1 (EC 1.1.1.41)	protein	338	41% helix, 23% strand	P28834
H, L	Isocitrate dehydrogenase [NAD] subunit 2 (EC 1.1.1.41)	protein	346	40% helix, 20% strand	P28241
K	Isocitrate dehydrogenase [NAD] subunit 1 (EC 1.1.1.41)	protein	337	41% helix, 23% strand	P28834
M	Isocitrate dehydrogenase [NAD] subunit 1 (EC 1.1.1.41)	protein	339	41% helix, 23% strand	P28834
O	Isocitrate dehydrogenase [NAD] subunit 1 (EC 1.1.1.41)	protein	330	42% helix, 22% strand	P28834

Ligands and binding sites

AMP · Adenosine monophosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
FLC · Citrate anion · additive · 8 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P

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	918	0.75	0.78	81	empty
2	538	0.74	0.82	67	FLC, AMP
3	512	0.73	0.82	68	FLC, AMP
4	516	0.73	0.82	66	FLC, AMP
5	529	0.73	0.81	70	FLC, AMP

Interfaces

34 interfaces between chains.

C–D · 2307 Å² buried · 32 hydrogen bonds · protein-protein
O–P · 2303 Å² buried · 34 hydrogen bonds · protein-protein
M–N · 2301 Å² buried · 32 hydrogen bonds · protein-protein
E–F · 2300 Å² buried · 34 hydrogen bonds · protein-protein
K–L · 2299 Å² buried · 34 hydrogen bonds · protein-protein

Compared structures

3BLW · Yeast Isocitrate Dehydrogenase with Citrate and AMP Bound in the Regulatory Subunits · the same entry in another collection · chain P against P, 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 P28834
Every structure of UniProt P28241
Elsewhere: RCSB PDB 3BLW · PDBe 3BLW · UniProt P28834 · UniProt P28241

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