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Crystal structure of apo dipeptide epimerase from thermotoga maritima

Analyse Crystal structure of apo dipeptide epimerase from thermotoga maritima in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3DFY
Type: protein
Length: 5,327 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Muconate cycloisomerase
UniProt: Q9WXM1
Ligands: MG
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 7 distinct chains · 44% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, I, M	Muconate cycloisomerase	protein	338	42% helix, 23% strand	Q9WXM1
B, D, P	Muconate cycloisomerase	protein	332	44% helix, 20% strand	Q9WXM1
E, G, K	Muconate cycloisomerase	protein	330	44% helix, 21% strand	Q9WXM1
F	Muconate cycloisomerase	protein	333	44% helix, 20% strand	Q9WXM1
H, J	Muconate cycloisomerase	protein	331	44% helix, 21% strand	Q9WXM1
L, O	Muconate cycloisomerase	protein	331	44% helix, 21% strand	Q9WXM1
N	Muconate cycloisomerase	protein	332	45% helix, 20% strand	Q9WXM1

Ligands and binding sites

MG · Magnesium ion · metal · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P

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	1083	0.87	0.88	135	empty
2	939	0.87	0.88	120	empty
3	928	0.86	0.88	120	empty
4	940	0.86	0.88	119	empty
5	657	0.86	0.90	95	empty

Interfaces

40 interfaces between chains.

E–F · 1363 Å² buried · 23 hydrogen bonds · protein-protein
K–L · 1363 Å² buried · 26 hydrogen bonds · protein-protein
I–J · 1359 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 1349 Å² buried · 25 hydrogen bonds · protein-protein
M–N · 1348 Å² buried · 25 hydrogen bonds · protein-protein

Compared structures

3DFY · Crystal structure of apo dipeptide epimerase from Thermotoga maritima · the same entry in another collection · chain K against K, 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 Q9WXM1
Elsewhere: RCSB PDB 3DFY · PDBe 3DFY · UniProt Q9WXM1

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