SMTL ID : 8ros.1

human pyridoxine 5-phosphate oxidase in complex with Z isomer of pyridoxilidenrhodanine 5-phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 17 residues within 4Å: Chain A: R.98, M.99, L.100, L.101, F.113, T.114, S.118, R.119, K.120, Q.177, S.178 Chain B: Y.135, Q.142, R.144, W.222, R.232 Ligands: 01.2 23 PLIP interactions: 10 interactions with chain B, 13 interactions with chain A Hydrophobic interactions: B:Y.135, B:W.222, B:W.222, A:M.99 Hydrogen bonds: B:Q.142, B:W.222, A:M.99, A:M.99, A:L.101, A:F.113, A:R.119, A:K.120, A:K.120, A:Q.177, A:S.178 Water bridges: B:R.144, B:R.144, B:R.144, A:R.119 Salt bridges: B:R.144, B:R.232, A:R.98, A:K.120 FMN.6: 17 residues within 4Å: Chain A: Y.135, Q.142, R.144, W.222, R.232 Chain B: R.98, M.99, L.100, L.101, F.113, T.114, S.118, R.119, K.120, Q.177, S.178 Ligands: 01.7 24 PLIP interactions: 10 interactions with chain A, 14 interactions with chain B Hydrophobic interactions: A:Y.135, A:W.222, A:W.222, B:M.99 Hydrogen bonds: A:Q.142, A:W.222, B:M.99, B:M.99, B:L.101, B:F.113, B:T.114, B:R.119, B:K.120, B:K.120, B:Q.177, B:S.178 Water bridges: A:R.144, A:R.144, A:R.144, B:R.119 Salt bridges: A:R.144, A:R.232, B:R.98, B:K.120

2 x 01: [6-methyl-5-oxidanylidene-4-[(4-oxidanylidene-2-sulfanylidene-1,3-thiazol-5-yl)methyl]-4~{H}-pyridin-3-yl]methyl dihydrogen phosphate

01.2: 12 residues within 4Å: Chain A: E.80, L.101, K.103, Y.160, R.164, Q.177 Chain B: N.140, W.222, R.228, H.230, P.264 Ligands: FMN.1 12 PLIP interactions: 7 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:R.228 Water bridges: B:R.228, B:R.228, B:R.228, B:R.228 Salt bridges: B:R.228, A:K.103, A:R.164 pi-Cation interactions: B:R.228 Hydrogen bonds: A:E.80, A:Y.160, A:R.164 01.7: 12 residues within 4Å: Chain A: N.140, W.222, R.228, H.230, P.264 Chain B: E.80, L.101, K.103, Y.160, R.164, Q.177 Ligands: FMN.6 13 PLIP interactions: 7 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:R.228 Water bridges: A:R.228, A:R.228, A:R.228, A:R.228, B:R.164 Salt bridges: A:R.228, B:K.103, B:R.164 pi-Cation interactions: A:R.228 Hydrogen bonds: B:E.80, B:Y.160, B:Y.160

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 10 residues within 4Å: Chain A: E.80, A.81, A.83, M.84, M.99, V.133, F.134, Y.135, W.136 Ligands: PEG.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.85, A:Y.135, A:W.136 PEG.4: 6 residues within 4Å: Chain A: E.117, S.118, R.119, K.122, E.123, S.178 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.177 Water bridges: A:K.122, A:E.123, A:S.179 PEG.8: 10 residues within 4Å: Chain B: E.80, A.81, A.83, M.84, M.99, V.133, F.134, Y.135, W.136 Ligands: PEG.3 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:C.85, B:Y.135, B:W.136 PEG.9: 6 residues within 4Å: Chain B: E.117, S.118, R.119, K.122, E.123, S.178 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.177 Water bridges: B:K.122, B:S.179

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

NA.5: 3 residues within 4Å: Chain A: Y.215, R.237, D.256 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.237, A:D.256 NA.10: 3 residues within 4Å: Chain B: Y.215, R.237, D.256 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.215, B:R.237, B:D.256

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ilari, A. et al., Pyridoxine 5-phosphate oxidase in complex with pyridoxilidenrhodanine 5-phosphate. To Be Published

Release Date

2025-01-29

Peptides

Pyridoxine-5'-phosphate oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
AAA

Pyridoxine-5'-phosphate oxidase

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