MolNFT v1 · #120611 · protein

Crystal structure of NADH bound carbonyl reductase from streptomyces coelicolor

5H5X · Putative oxidoreductase: “Crystal structure of NADH bound carbonyl reductase from streptomyces coelicolor”. X-ray diffraction, 2 ligands (NAI, MG), 20 pockets (best druggability 0.86). MolNFT v1 #120611 on GenesisL1: 3D structure…

PDB: 5H5X
Type: protein
Length: 3,017 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative oxidoreductase
UniProt: Q9KYM4
Ligands: NAI, MG
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 8 distinct chains · 49% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative oxidoreductase	protein	248	49% helix, 16% strand	Q9KYM4
B, F, J	Putative oxidoreductase	protein	253	50% helix, 16% strand	Q9KYM4
C, G, K	Putative oxidoreductase	protein	257	50% helix, 16% strand	Q9KYM4
D	Putative oxidoreductase	protein	250	50% helix, 16% strand	Q9KYM4
E	Putative oxidoreductase	protein	248	50% helix, 17% strand	Q9KYM4
H	Putative oxidoreductase	protein	252	47% helix, 16% strand	Q9KYM4
I	Putative oxidoreductase	protein	243	51% helix, 16% strand	Q9KYM4
L	Putative oxidoreductase	protein	246	48% helix, 15% strand	Q9KYM4

Ligands and binding sites

NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
MG · Magnesium ion · metal · 6 copies · chains A, C, B, D, E, G, F, H, I, K, J, L
IPA · Isopropyl alcohol · additive · 22 copies · chains A, B, C, D, E, F, G, H, I, J, K, L

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

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	843	0.86	0.89	52	empty
2	868	0.86	0.88	53	empty
3	861	0.86	0.88	56	empty
4	503	0.69	0.79	42	NAI, IPA
5	458	0.69	0.80	45	NAI, IPA

Interfaces

21 interfaces between chains.

C–D · 1599 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 1596 Å² buried · 23 hydrogen bonds · protein-protein
K–L · 1595 Å² buried · 25 hydrogen bonds · protein-protein
G–H · 1595 Å² buried · 28 hydrogen bonds · protein-protein
E–F · 1587 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

5H5X · Crystal structure of NADH bound carbonyl reductase from Streptomyces coelicolor · 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 Q9KYM4
Elsewhere: RCSB PDB 5H5X · PDBe 5H5X · UniProt Q9KYM4

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