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2.39 ångström X-ray crystal structure of human acmsd

Analyse 2.39 ångström X-ray crystal structure of human acmsd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4IGM
Type: protein
Length: 1,992 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
EC: 4.1.1.45
UniProt: Q8TDX5
Ligands: ZN
Pockets: 20 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 44% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	2-amino-3-carboxymuconate-6-semialdehyde decarboxylase (EC 4.1.1.45)	protein	332	44% helix, 17% strand	Q8TDX5

Ligands and binding sites

ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F

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

Pockets

20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	827	0.75	0.79	44	empty
2	471	0.68	0.79	61	empty
3	234	0.67	0.84	24	empty
4	398	0.67	0.80	65	empty
5	241	0.66	0.84	21	empty

Interfaces

6 interfaces between chains.

A–F · 2548 Å² buried · 42 hydrogen bonds · protein-protein
B–C · 2544 Å² buried · 36 hydrogen bonds · protein-protein
D–E · 2526 Å² buried · 29 hydrogen bonds · protein-protein
A–B · 478 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 181 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

4IGM · 2.39 Angstrom X-ray Crystal structure of human ACMSD · the same entry in another collection · chain F against F, TM-score 1.00
Q8TDX5 · AlphaFold monomer V2.0 prediction for 2-amino-3-carboxymuconate-6-semialdehyde… · a predicted model of the same protein · chain E against A, TM-score 0.99

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 Q8TDX5
Elsewhere: RCSB PDB 4IGM · PDBe 4IGM · UniProt Q8TDX5

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