MolNFT v1 · #25159 · protein

Crystal structure of a putative KHG/KDPG aldolase

1VHC: “Crystal structure of a putative KHG/KDPG aldolase”. X-ray diffraction, 18 pockets (best druggability 0.63). MolNFT v1 #25159 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1VHC
Type: protein
Length: 1,273 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative KHG/KDPG aldolase
UniProt: P44480
Pockets: 18 · best druggability 0.63

Structure

x-ray diffraction · 2 distinct chains · 47% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	Putative KHG/KDPG aldolase	protein	212	47% helix, 17% strand	P44480
F	Putative KHG/KDPG aldolase	protein	213	47% helix, 16% strand	P44480

Pockets

18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	235	0.63	0.82	31	empty
2	230	0.61	0.81	33	empty
3	504	0.60	0.74	49	empty
4	410	0.59	0.75	48	empty
5	246	0.59	0.79	30	empty

Interfaces

12 interfaces between chains.

A–B · 685 Å² buried · 3 hydrogen bonds · protein-protein
D–F · 684 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 674 Å² buried · 8 hydrogen bonds · protein-protein
E–F · 665 Å² buried · 4 hydrogen bonds · protein-protein
D–E · 648 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 modified (engineered).

Compared structures

1VHC · Crystal structure of a putative KHG/KDPG aldolase · the same entry in another collection · chain E against E, TM-score 1.00
P44480 · AlphaFold monomer V2.0 prediction for putative KHG/KDPG aldolase (P44480) · a predicted model of the same protein · chain D 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 P44480
Elsewhere: RCSB PDB 1VHC · PDBe 1VHC · UniProt P44480

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