SMTL ID : 5vxa.3 (2 other biounits)

Structure of the human Mesh1-NADPH complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.36, H.62, D.63, D.123 Ligands: NDP.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.36, A:H.62, A:D.63, A:D.123, H2O.1 ZN.7: 5 residues within 4Å: Chain B: H.36, H.62, D.63, D.123 Ligands: NDP.8 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.36, B:H.62, B:D.63, B:D.123, H2O.5

2 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.2: 23 residues within 4Å: Chain A: R.25, K.26, D.27, Y.33, H.36, D.63, E.66, K.67, K.98, L.99, K.102, D.123, N.127, D.130, L.131, W.139, S.140, H.142, R.143, E.146, Y.147 Ligands: ZN.1, NA.6 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:R.143 Hydrogen bonds: A:R.25, A:K.26, A:D.27, A:N.127, A:D.130, A:S.140, A:H.142, A:R.143, A:Y.147 Water bridges: A:E.66, A:E.66, A:K.67, A:K.67, A:D.130, A:R.133, A:R.133 Salt bridges: A:R.25, A:K.26, A:K.26, A:H.36, A:K.67, A:K.98, A:K.102, A:R.143 pi-Cation interactions: A:R.25, A:R.25, A:R.143 NDP.8: 18 residues within 4Å: Chain B: R.25, K.26, D.27, Y.33, H.36, D.63, E.66, K.67, K.98, K.102, D.123, N.127, D.130, L.131, W.139, R.143, Y.147 Ligands: ZN.7 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:R.25, B:R.25, B:K.26, B:Y.33, B:D.123, B:N.127, B:Y.147 Water bridges: B:K.26, B:K.26, B:K.26, B:K.67, B:D.130, B:R.133, B:R.133, B:R.143, B:R.143 Salt bridges: B:H.36, B:K.67, B:K.102, B:K.102, B:R.143 pi-Cation interactions: B:R.25, B:R.25

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 3 residues within 4Å: Chain A: E.11, H.78 Chain B: R.42 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.11, B:R.42 EDO.4: 5 residues within 4Å: Chain A: V.65, E.66, T.91, D.92, K.94 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.68, A:D.92, A:K.94 EDO.9: 2 residues within 4Å: Chain B: Q.23, R.24 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.24

2 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.5: 3 residues within 4Å: Chain A: E.29, R.133, C.134 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.29 BME.10: 2 residues within 4Å: Chain B: R.133, C.134 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.133

1 x NA: SODIUM ION(Non-functional Binders)

NA.6: 1 residues within 4Å: Ligands: NDP.2 No protein-ligand interaction detected (PLIP)

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.11: 0 residues within 4Å: (No contacts) 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.129, B:R.129

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ding, C.C. et al., MESH1 is a cytosolic NADPH phosphatase that regulates ferroptosis. Nat Metab (2020)

Release Date

2018-05-23

Peptides

Guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase MESH1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase MESH1

Related Entries With Identical Sequence