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Renalase in complex with NADH

Analyse Renalase in complex with NADH in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4ZCC
Type: protein
Length: 1,288 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Renalase
EC: 1.6.3.5
UniProt: Q48MT7
Ligands: FAD, NAI
Pockets: 11 · best druggability 0.87

Structure

x-ray diffraction · 4 distinct chains · 30% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Renalase (EC 1.6.3.5)	protein	320	30% helix, 29% strand	Q48MT7
B	Renalase (EC 1.6.3.5)	protein	319	30% helix, 29% strand	Q48MT7
C	Renalase (EC 1.6.3.5)	protein	321	31% helix, 30% strand	Q48MT7
D	Renalase (EC 1.6.3.5)	protein	328	30% helix, 29% strand	Q48MT7

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
FMT · Formic acid · additive · 4 copies · chains A, B, C, D

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

Pockets

11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1064	0.87	0.89	118	FAD
2	1028	0.87	0.89	126	FAD
3	121	0.59	0.85	27	empty
4	133	0.59	0.84	26	empty
5	283	0.58	0.78	31	empty

Interfaces

5 interfaces between chains.

B–C · 1273 Å² buried · 15 hydrogen bonds · protein-protein
A–D · 1249 Å² buried · 10 hydrogen bonds · protein-protein
B–D · 670 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 65 Å² buried · 3 hydrogen bonds · protein-protein
C–D · 63 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

4ZCC · Renalase in complex with NADH · the same entry in another collection · chain D against D, TM-score 1.00
Q48MT7 · AlphaFold monomer V2.0 prediction for renalase (Q48MT7) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 Q48MT7
Elsewhere: RCSB PDB 4ZCC · PDBe 4ZCC · UniProt Q48MT7

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