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Crystal structure of PDUOC:HEME complex

Analyse Crystal structure of PDUOC:HEME complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5CX7
Type: protein
Length: 2,209 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATP:COB(I)ALAMIN adenosyltransferase
UniProt: A0A0F0IPG3
Ligands: HEM, NA, MG, CL
Pockets: 20 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, F, G, H, I, J, K, L, M, N, O, P	ATP:COB(I)ALAMIN adenosyltransferase	protein	138	38% helix, 20% strand	A0A0F0IPG3
E	ATP:COB(I)ALAMIN adenosyltransferase	protein	139	38% helix, 20% strand	A0A0F0IPG3

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 8 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
NA · Sodium ion · metal · 18 copies · chains A, C, G, E, B, D, H, F, I, K, O, M, J, L, P, N
MG · Magnesium ion · metal · 2 copies · chains H, P
CL · Chloride ion · ion · 4 copies · chains A, C, E, G, B, D, F, H, I, K, M, O, J, L, N, P
GOL · Glycerol · additive · 25 copies · chains A, C, B, H, E, D, G, F, I, K, J, P, M, O, L, N

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	743	0.78	0.82	98	empty
2	338	0.68	0.82	47	HEM
3	298	0.67	0.82	53	empty
4	387	0.67	0.80	51	HEM
5	133	0.63	0.86	19	HEM

Interfaces

40 interfaces between chains.

A–G · 805 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 801 Å² buried · 11 hydrogen bonds · protein-protein
B–H · 801 Å² buried · 11 hydrogen bonds · protein-protein
E–G · 801 Å² buried · 12 hydrogen bonds · protein-protein
J–P · 800 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

5CX7 · Crystal Structure of PduOC:Heme Complex · 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 A0A0F0IPG3
Elsewhere: RCSB PDB 5CX7 · PDBe 5CX7 · UniProt A0A0F0IPG3

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