MolNFT v1 · #47843 · protein

Crystal structure of E. COLI glyoxylate carboligase

2PAN: “Crystal structure of E. COLI glyoxylate carboligase”. X-ray diffraction, 3 ligands (FAD, TPP, MG), 20 pockets (best druggability 0.85). MolNFT v1 #47843 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2PAN
Type: protein
Length: 3,552 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glyoxylate carboligase
EC: 4.1.1.47
UniProt: P0AEP7
Ligands: FAD, TPP, MG
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Glyoxylate carboligase (EC 4.1.1.47)	protein	592	42% helix, 17% strand	P0AEP7

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · 6 copies · chains A, B, C, E, D, F
TPP · Thiamine diphosphate · ligand · 6 copies · chains A, B, C, E, D, F
MG · Magnesium ion · metal · 10 copies · chains A, B, C, D, E, F
DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 6 copies · chains A, B, C, D, E, F
1PE · Pentaethylene glycol · additive · chains A

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	454	0.85	0.92	68	FAD
2	436	0.85	0.93	71	FAD
3	451	0.84	0.92	73	FAD
4	418	0.84	0.92	71	FAD
5	494	0.82	0.89	69	FAD

Interfaces

8 interfaces between chains.

D–F · 4054 Å² buried · 60 hydrogen bonds · protein-protein
C–E · 4031 Å² buried · 61 hydrogen bonds · protein-protein
C–D · 1636 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 1618 Å² buried · 11 hydrogen bonds · protein-protein
E–F · 1605 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 132 modified (engineered).

Compared structures

2PAN · Crystal structure of E. coli glyoxylate carboligase · the same entry in another collection · chain F against F, TM-score 1.00
P0AEP7 · AlphaFold monomer V2.0 prediction for glyoxylate carboligase (P0AEP7) · a predicted model of the same protein · chain F against A, 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 P0AEP7
Elsewhere: RCSB PDB 2PAN · PDBe 2PAN · UniProt P0AEP7

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