SMTL ID : 3wev.2 (1 other biounit)

Crystal structure of the Schiff base intermediate of L-Lys epsilon-oxidase from Marinomonas mediterranea with L-Lys

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-tetramer

Ligands

4 x LYS: LYSINE(Covalent)

LYS.1: 8 residues within 4Å: Chain A: V.386, C.448, P.449, N.515, Q.519, K.530, W.580, W.581 9 PLIP interactions: 8 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:V.386, A:N.515 Hydrogen bonds: A:G.450, A:Q.519, A:Q.519, K.1 Water bridges: A:N.515, A:Q.519 Salt bridges: A:K.530 LYS.11: 8 residues within 4Å: Chain B: V.386, C.448, P.449, N.515, Q.519, K.530, W.580, W.581 11 PLIP interactions: 10 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:V.386, B:N.515, B:W.580 Hydrogen bonds: B:Q.519, B:Q.519, K.11 Water bridges: B:N.515, B:I.518, B:Q.519, B:Q.519 Salt bridges: B:K.530 LYS.21: 8 residues within 4Å: Chain C: V.386, C.448, P.449, N.515, Q.519, K.530, W.580, W.581 9 PLIP interactions: 8 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: C:V.386, C:N.515 Hydrogen bonds: C:G.450, C:Q.519, C:Q.519, K.21 Water bridges: C:N.515, C:Q.519 Salt bridges: C:K.530 LYS.31: 8 residues within 4Å: Chain D: V.386, C.448, P.449, N.515, Q.519, K.530, W.580, W.581 11 PLIP interactions: 10 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: D:V.386, D:N.515, D:W.580 Hydrogen bonds: D:Q.519, D:Q.519, K.31 Water bridges: D:N.515, D:I.518, D:Q.519, D:Q.519 Salt bridges: D:K.530

10 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 3 residues within 4Å: Chain A: E.98, F.99, R.122 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.99 Water bridges: A:E.98 Salt bridges: A:R.122 SO4.3: 2 residues within 4Å: Chain A: H.286, Y.287 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.287 Salt bridges: A:H.286 SO4.4: 2 residues within 4Å: Chain A: G.109, R.110 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.110 Water bridges: A:D.111, A:D.111 Salt bridges: A:R.110 SO4.12: 3 residues within 4Å: Chain B: G.285, H.286, Y.287 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.287 Salt bridges: B:H.286 SO4.13: 2 residues within 4Å: Chain B: G.109, R.110 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.110 Water bridges: B:D.111 Salt bridges: B:R.110 SO4.22: 3 residues within 4Å: Chain C: E.98, F.99, R.122 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:F.99 Salt bridges: C:R.122 SO4.23: 2 residues within 4Å: Chain C: H.286, Y.287 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.287 Salt bridges: C:H.286 SO4.24: 2 residues within 4Å: Chain C: G.109, R.110 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.110 Water bridges: C:D.111, C:D.111 Salt bridges: C:R.110 SO4.32: 3 residues within 4Å: Chain D: G.285, H.286, Y.287 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.287 Salt bridges: D:H.286 SO4.33: 2 residues within 4Å: Chain D: G.109, R.110 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.110 Water bridges: D:D.111 Salt bridges: D:R.110

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

EDO.5: 6 residues within 4Å: Chain A: L.106, L.107, N.459, P.460, V.461, C.490 Ligand excluded by PLIP EDO.6: 3 residues within 4Å: Chain A: Y.577, W.587, N.611 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain A: N.21, D.51, E.52 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: I.29, V.256, P.301, R.305 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: R.271, L.349, K.352, A.407 Ligands: EDO.10 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: R.271, Y.280, G.285 Ligands: EDO.9 Ligand excluded by PLIP EDO.15: 2 residues within 4Å: Chain B: N.515, Y.619 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain B: L.106, L.107, N.459, P.460, V.461, C.490 Ligand excluded by PLIP EDO.17: 3 residues within 4Å: Chain B: N.21, D.51, E.52 Ligand excluded by PLIP EDO.18: 3 residues within 4Å: Chain B: S.432, D.433, M.434 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain B: I.29, V.256, P.301, R.305 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain B: R.329, G.331, F.421, A.423 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain C: L.106, L.107, N.459, P.460, V.461, C.490 Ligand excluded by PLIP EDO.26: 3 residues within 4Å: Chain C: Y.577, W.587, N.611 Ligand excluded by PLIP EDO.27: 3 residues within 4Å: Chain C: N.21, D.51, E.52 Ligand excluded by PLIP EDO.28: 4 residues within 4Å: Chain C: I.29, V.256, P.301, R.305 Ligand excluded by PLIP EDO.29: 5 residues within 4Å: Chain C: R.271, L.349, K.352, A.407 Ligands: EDO.30 Ligand excluded by PLIP EDO.30: 4 residues within 4Å: Chain C: R.271, Y.280, G.285 Ligands: EDO.29 Ligand excluded by PLIP EDO.35: 2 residues within 4Å: Chain D: N.515, Y.619 Ligand excluded by PLIP EDO.36: 6 residues within 4Å: Chain D: L.106, L.107, N.459, P.460, V.461, C.490 Ligand excluded by PLIP EDO.37: 3 residues within 4Å: Chain D: N.21, D.51, E.52 Ligand excluded by PLIP EDO.38: 3 residues within 4Å: Chain D: S.432, D.433, M.434 Ligand excluded by PLIP EDO.39: 4 residues within 4Å: Chain D: I.29, V.256, P.301, R.305 Ligand excluded by PLIP EDO.40: 4 residues within 4Å: Chain D: R.329, G.331, F.421, A.423 Ligand excluded by PLIP

2 x DIO: 1,4-DIETHYLENE DIOXIDE(Non-covalent)

DIO.14: 7 residues within 4Å: Chain B: G.615, N.617, P.677, V.678, F.679 Chain D: V.662, L.676 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.679 Water bridges: B:N.617, B:N.617 DIO.34: 7 residues within 4Å: Chain B: V.662, L.676 Chain D: G.615, N.617, P.677, V.678, F.679 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:F.679 Water bridges: D:N.617, D:N.617

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Okazaki, S. et al., X-Ray crystallographic evidence for the presence of the cysteine tryptophylquinone cofactor in L-lysine {varepsilon}-oxidase from Marinomonas mediterranea. J.Biochem. (2013)

Release Date

2013-09-04

Peptides

L-lysine 6-oxidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

L-lysine 6-oxidase

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