MolNFT v1 · #145421 · protein

Crystal structure of H105A PGAM5 dodecamer

6CNL · SERINE/THREONINE-protein phosphatase PGAM5, mitochondrial: “Crystal structure of H105A PGAM5 dodecamer”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.64). MolNFT v1 #145421 on GenesisL1: 3D structure, binding…

PDB: 6CNL
Type: protein
Length: 2,379 residues
Chains: 24
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: SERINE/THREONINE-protein phosphatase PGAM5, mitochondrial; PGAM5 multimerization motif…
EC: 3.1.3.16
UniProt: Q96HS1
Ligands: MG
Pockets: 20 · best druggability 0.64

Structure

x-ray diffraction · 15 distinct chains · 35% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	SERINE/THREONINE-protein phosphatase PGAM5, mitochondrial (EC 3.1.3.16)	protein	186	36% helix, 22% strand	Q96HS1
C	SERINE/THREONINE-protein phosphatase PGAM5, mitochondrial (EC 3.1.3.16)	protein	189	35% helix, 22% strand	Q96HS1
L	SERINE/THREONINE-protein phosphatase PGAM5, mitochondrial (EC 3.1.3.16)	protein	192	36% helix, 21% strand	Q96HS1
J	SERINE/THREONINE-protein phosphatase PGAM5, mitochondrial (EC 3.1.3.16)	protein	184	36% helix, 22% strand	Q96HS1
F	SERINE/THREONINE-protein phosphatase PGAM5, mitochondrial (EC 3.1.3.16)	protein	187	36% helix, 22% strand	Q96HS1
H	SERINE/THREONINE-protein phosphatase PGAM5, mitochondrial (EC 3.1.3.16)	protein	186	36% helix, 22% strand	Q96HS1
K	SERINE/THREONINE-protein phosphatase PGAM5, mitochondrial (EC 3.1.3.16)	protein	187	36% helix, 22% strand	Q96HS1
D	SERINE/THREONINE-protein phosphatase PGAM5, mitochondrial (EC 3.1.3.16)	protein	191	35% helix, 21% strand	Q96HS1
B	SERINE/THREONINE-protein phosphatase PGAM5, mitochondrial (EC 3.1.3.16)	protein	188	35% helix, 22% strand	Q96HS1
I	SERINE/THREONINE-protein phosphatase PGAM5, mitochondrial (EC 3.1.3.16)	protein	183	37% helix, 22% strand	Q96HS1
G	SERINE/THREONINE-protein phosphatase PGAM5, mitochondrial (EC 3.1.3.16)	protein	189	35% helix, 22% strand	Q96HS1
E	SERINE/THREONINE-protein phosphatase PGAM5, mitochondrial (EC 3.1.3.16)	protein	187	35% helix, 22% strand	Q96HS1
M, O, V, R, T, W, P, N, U, S	PGAM5 multimerization motif peptide	protein	11	0% helix, 0% strand	—
X	PGAM5 multimerization motif peptide	protein	10	0% helix, 0% strand	—
Q	PGAM5 multimerization motif peptide	protein	10	0% helix, 0% strand	—

Ligands and binding sites

MG · Magnesium ion · metal · 31 copies · chains A, C, O, L, J, F, G, E, H, K, D, B, I, 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, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	189	0.64	0.84	20	empty
2	166	0.63	0.84	17	empty
3	181	0.61	0.83	20	empty
4	179	0.61	0.83	21	empty
5	166	0.60	0.83	20	empty

Interfaces

48 interfaces between chains.

C–D · 1317 Å² buried · 39 hydrogen bonds · protein-protein
H–G · 1299 Å² buried · 36 hydrogen bonds · protein-protein
L–K · 1294 Å² buried · 41 hydrogen bonds · protein-protein
A–B · 1284 Å² buried · 36 hydrogen bonds · protein-protein
F–E · 1263 Å² buried · 37 hydrogen bonds · protein-protein

Compared structures

6CNL · Crystal Structure of H105A PGAM5 Dodecamer · the same entry in another collection · chain G against G, 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 Q96HS1
Elsewhere: RCSB PDB 6CNL · PDBe 6CNL · UniProt Q96HS1

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