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Crystal structure of ignicoccus islandicus malate dehydrogenase co- crystallized with 10 mm tb-XO4

Analyse Crystal structure of ignicoccus islandicus malate dehydrogenase co… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6QSS
Type: protein
Length: 1,214 residues
Chains: 4
Method: x-ray diffraction; solution scattering
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Malate dehydrogenase
UniProt: A0A0U3FQH7
Ligands: 7MT, TB, CL
Pockets: 19 · best druggability 0.87

Structure

x-ray diffraction; solution scattering · 4 distinct chains · 48% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Malate dehydrogenase	protein	303	49% helix, 24% strand	A0A0U3FQH7
B	Malate dehydrogenase	protein	307	47% helix, 25% strand	A0A0U3FQH7
C	Malate dehydrogenase	protein	305	48% helix, 24% strand	A0A0U3FQH7
D	Malate dehydrogenase	protein	299	49% helix, 26% strand	A0A0U3FQH7

Ligands and binding sites

7MT · Tb-Xo4 · ligand · 2 copies · chains A, D
TB · Terbium(iii) ion · metal · 18 copies · chains A, B, C, D
CL · Chloride ion · ion · 3 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1078	0.87	0.88	74	empty
2	574	0.69	0.78	50	empty
3	658	0.68	0.77	72	empty
4	529	0.67	0.78	50	CL
5	294	0.61	0.79	34	empty

Interfaces

6 interfaces between chains.

C–D · 2108 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 2033 Å² buried · 16 hydrogen bonds · protein-protein
A–D · 1285 Å² buried · 17 hydrogen bonds · protein-protein
B–C · 1278 Å² buried · 16 hydrogen bonds · protein-protein
A–C · 635 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

6QSS · Crystal Structure of Ignicoccus islandicus malate dehydrogenase co-crystallized with 10… · the same entry in another collection · chain D against D, 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 A0A0U3FQH7
Elsewhere: RCSB PDB 6QSS · PDBe 6QSS · UniProt A0A0U3FQH7

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