SMTL ID : 3r7c.3 (2 other biounits)

The structure of a hexahestidine-tagged form of augmenter of liver regeneration reveals a novel Cd(2)Cl(4)O(6) cluster that aids in crystal packing

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

4 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 25 residues within 4Å: Chain A: R.33, E.34, G.37, R.38, T.40, W.41, H.45, F.70, Y.74, C.76, C.79, A.80, E.81, I.83, C.105, H.108, N.109, V.111, N.112, L.115, K.117, F.120, R.128, W.129 Chain C: D.28 26 PLIP interactions: 23 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:T.40, A:W.41, A:W.41, A:F.70, A:Y.74, A:I.83 Hydrogen bonds: A:W.41, A:W.41, A:A.80, A:E.81, A:N.112, A:N.112, A:K.117, A:R.128, C:D.28 Water bridges: A:R.33, A:R.33, A:E.34, C:D.28, C:D.28 Salt bridges: A:R.38, A:H.108, A:K.117 pi-Stacking: A:H.108, A:F.120, A:F.120 FAD.10: 25 residues within 4Å: Chain B: R.33, E.34, G.37, R.38, T.40, W.41, H.45, F.70, Y.74, C.76, C.79, A.80, E.81, I.83, C.105, H.108, N.109, V.111, N.112, L.115, K.117, F.120, V.125, R.128, W.129 22 PLIP interactions: 21 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:T.40, B:W.41, B:W.41, B:F.70, B:Y.74, B:I.83 Hydrogen bonds: B:R.33, B:W.41, B:W.41, B:A.80, B:E.81, B:C.105, B:N.112, B:K.117, B:R.128 Salt bridges: B:R.38, B:H.108, B:K.117 pi-Stacking: B:H.108, B:F.120, B:F.120 Water bridges: D:D.28 FAD.15: 23 residues within 4Å: Chain C: R.33, E.34, G.37, R.38, T.40, W.41, H.45, F.70, Y.74, C.79, I.83, C.105, H.108, N.109, V.111, N.112, K.114, L.115, K.117, F.120, V.125, R.128, W.129 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:W.41, C:W.41, C:W.41, C:F.70 Hydrogen bonds: C:W.41, C:W.41, C:C.105, C:H.108, C:N.112, C:K.114, C:K.117, C:R.128 Water bridges: C:K.114 Salt bridges: C:R.38, C:H.108, C:K.117 pi-Stacking: C:Y.74, C:H.108, C:F.120, C:F.120 FAD.18: 24 residues within 4Å: Chain D: R.33, E.34, G.37, R.38, T.40, W.41, H.45, F.70, Y.74, C.76, C.79, A.80, E.81, I.83, C.105, H.108, N.109, V.111, N.112, L.115, K.117, F.120, R.128, W.129 23 PLIP interactions: 23 interactions with chain D Hydrophobic interactions: D:T.40, D:W.41, D:F.70, D:Y.74, D:I.83 Hydrogen bonds: D:R.38, D:W.41, D:W.41, D:A.80, D:E.81, D:C.105, D:H.108, D:N.112, D:K.117, D:R.128 Water bridges: D:R.33, D:E.78 Salt bridges: D:H.108, D:K.117, D:K.117 pi-Stacking: D:H.108, D:F.120, D:F.120

10 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 2 residues within 4Å: Chain A: E.58, Q.61 Ligand excluded by PLIP CL.3: 4 residues within 4Å: Chain A: E.58, D.62 Chain B: R.89 Chain C: K.72 Ligand excluded by PLIP CL.6: 8 residues within 4Å: Chain A: H.68, K.72 Chain B: D.88 Ligands: CD.4, CD.5, CL.7, CL.8, CL.9 Ligand excluded by PLIP CL.7: 8 residues within 4Å: Chain A: D.88 Chain B: H.68, K.72 Ligands: CD.4, CD.5, CL.6, CL.8, CL.9 Ligand excluded by PLIP CL.8: 7 residues within 4Å: Chain A: K.72, R.84, D.88 Chain B: K.72 Ligands: CD.4, CL.6, CL.7 Ligand excluded by PLIP CL.9: 7 residues within 4Å: Chain A: K.72 Chain B: K.72, R.84, D.88 Ligands: CD.5, CL.6, CL.7 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain B: C.29, Q.31, E.35 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain B: R.86, R.106 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain C: Q.31, N.39 Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain D: E.35 Ligands: SO4.21 Ligand excluded by PLIP

5 x CD: CADMIUM ION(Non-covalent)

CD.4: 5 residues within 4Å: Chain A: D.88 Ligands: CD.5, CL.6, CL.7, CL.8 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.88, A:D.88, H2O.1 CD.5: 5 residues within 4Å: Chain B: D.88 Ligands: CD.4, CL.6, CL.7, CL.9 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.88, B:D.88, H2O.1 CD.11: 1 residues within 4Å: Chain B: E.127 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.127, H2O.3, H2O.4 CD.12: 2 residues within 4Å: Chain B: E.58, Q.61 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.58, H2O.1, H2O.4 CD.16: 2 residues within 4Å: Chain C: D.121, S.123 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.121, C:D.121, H2O.6, H2O.6

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

SO4.19: 2 residues within 4Å: Chain D: V.98, D.126 No protein-ligand interaction detected (PLIP) SO4.21: 3 residues within 4Å: Chain D: Q.31, N.39 Ligands: CL.20 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Florence, Q.J. et al., The structure of a hexahestidine-tagged form of augmenter of liver regeneration reveals a novel Cd(2)Cl(4)O(6) cluster that aids in crystal packing. To be Published

Release Date

2012-03-28

Peptides

FAD-linked sulfhydryl oxidase ALR: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

FAD-linked sulfhydryl oxidase ALR

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