MolNFT v1 · #96929 · protein

Meab, a bacterial homolog of mmaa, in its apo form

4JYC · Methylmalonyl-CoA mutase accessory protein: “Meab, a bacterial homolog of mmaa, in its apo form”. X-ray diffraction, 1 ligand (GDP), 20 pockets (best druggability 0.71). MolNFT v1 #96929 on GenesisL1: 3D structure, binding sites and…

PDB: 4JYC
Type: protein
Length: 1,264 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Methylmalonyl-CoA mutase accessory protein
UniProt: C5AP93
Ligands: GDP
Pockets: 20 · best druggability 0.71

Structure

x-ray diffraction · 4 distinct chains · 55% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Methylmalonyl-CoA mutase accessory protein	protein	311	57% helix, 13% strand	C5AP93
B	Methylmalonyl-CoA mutase accessory protein	protein	315	57% helix, 12% strand	C5AP93
C	Methylmalonyl-CoA mutase accessory protein	protein	324	54% helix, 12% strand	C5AP93
D	Methylmalonyl-CoA mutase accessory protein	protein	314	54% helix, 12% strand	C5AP93

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · chains D

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

Pockets

20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1102	0.71	0.75	112	empty
2	600	0.71	0.79	63	empty
3	589	0.67	0.77	67	empty
4	400	0.63	0.78	57	empty
5	260	0.59	0.79	37	empty

Interfaces

5 interfaces between chains.

B–C · 2550 Å² buried · 23 hydrogen bonds · protein-protein
A–D · 2338 Å² buried · 25 hydrogen bonds · protein-protein
B–D · 522 Å² buried · 1 hydrogen bond · protein-protein
A–C · 497 Å² buried · 2 hydrogen bonds · protein-protein
C–D · 389 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

4JYC · MeaB, A Bacterial Homolog of MMAA, in its Apo form · the same entry in another collection · chain A 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 C5AP93
Elsewhere: RCSB PDB 4JYC · PDBe 4JYC · UniProt C5AP93

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