MolNFT v1 · #77748 · protein

Crystal structure of dipeptide epimerase from methylococcus capsulatus complexed with mg ion

3RO6 · Putative chloromuconate cycloisomerase: “Crystal structure of dipeptide epimerase from methylococcus capsulatus complexed with mg ion”. X-ray diffraction, 2 ligands (MG, SO4), 14 pockets (best druggability 0.84). MolNFT v1 #77748 on…

PDB: 3RO6
Type: protein
Length: 2,067 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative chloromuconate cycloisomerase
UniProt: Q607C7
Ligands: MG, SO4
Pockets: 14 · best druggability 0.84

Structure

x-ray diffraction · 4 distinct chains · 42% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, E, F	Putative chloromuconate cycloisomerase	protein	344	41% helix, 23% strand	Q607C7
A	Putative chloromuconate cycloisomerase	protein	345	40% helix, 23% strand	Q607C7
C	Putative chloromuconate cycloisomerase	protein	346	42% helix, 23% strand	Q607C7
D	Putative chloromuconate cycloisomerase	protein	344	42% helix, 22% strand	Q607C7

Ligands and binding sites

MG · Magnesium ion · metal · 6 copies · chains B, A, C, D, E, F
SO4 · Sulfate ion · ion · 13 copies · chains B, A, C, D, E, F
GOL · Glycerol · additive · 2 copies · chains B, D

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

Pockets

14 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	924	0.84	0.85	78	empty
2	926	0.83	0.85	85	empty
3	857	0.68	0.74	87	GOL
4	445	0.58	0.75	41	SO4
5	299	0.58	0.77	38	empty

Interfaces

5 interfaces between chains.

D–E · 1289 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 1271 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 260 Å² buried · 8 hydrogen bonds · protein-protein
B–F · 208 Å² buried · 2 hydrogen bonds · protein-protein
B–A · 167 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3RO6 · Crystal structure of Dipeptide Epimerase from Methylococcus capsulatus complexed with Mg… · the same entry in another collection · chain F against F, TM-score 1.00
Q607C7 · AlphaFold monomer V2.0 prediction for L-lys-D/L-arg epimerase (Q607C7) · a predicted model of the same protein · chain D 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 Q607C7
Elsewhere: RCSB PDB 3RO6 · PDBe 3RO6 · UniProt Q607C7

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