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

Crystal Structure of Human Augmenter of Liver Regeneration (ALR)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 22 residues within 4Å: Chain A: R.33, E.34, G.37, R.38, S.40, W.41, H.45, Y.74, C.79, D.82, L.83, C.105, H.108, N.109, V.111, N.112, K.114, L.115, K.117, F.120, R.128, W.129 23 PLIP interactions: 21 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:W.41, A:W.41, A:W.41, A:L.83 Hydrogen bonds: A:R.33, A:R.38, A:R.38, A:W.41, A:C.105, A:N.112, A:K.114, A:K.114, A:K.117, A:R.128 Salt bridges: A:R.38, A:H.108, A:K.117, A:K.117 pi-Stacking: A:H.108, A:F.120, A:F.120 Water bridges: B:D.28, B:D.28 FAD.8: 22 residues within 4Å: Chain B: R.33, E.34, G.37, R.38, S.40, W.41, H.45, Y.74, C.79, D.82, L.83, C.105, H.108, N.109, V.111, N.112, K.114, L.115, K.117, F.120, R.128, W.129 27 PLIP interactions: 25 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:W.41, B:W.41, B:W.41, B:L.83 Hydrogen bonds: B:R.33, B:E.34, B:R.38, B:W.41, B:C.105, B:H.108, B:N.112, B:K.114, B:K.117, B:R.128 Water bridges: B:E.34, B:R.38, B:E.78, B:K.114, A:D.28, A:D.28 Salt bridges: B:R.38, B:H.108, B:K.117, B:K.117 pi-Stacking: B:H.108, B:F.120, B:F.120

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

NA.2: 1 residues within 4Å: Chain A: D.32 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.32 Water bridges: A:D.32 NA.10: 1 residues within 4Å: Chain B: D.32 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.32 Water bridges: B:D.32 NA.11: 3 residues within 4Å: Chain A: K.72 Chain B: E.58, D.62 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.62

6 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: E.35, H.39 Ligands: ACT.4, ACT.12 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Ligand interactions Metal complexes: A:E.35, A:H.39, ACT.4, ACT.12 ZN.6: 3 residues within 4Å: Chain A: H.68, H.91, P.92 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.68, A:H.91, H2O.4, H2O.4, H2O.4 ZN.7: 3 residues within 4Å: Chain A: H.106, E.110, R.113 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.106, A:E.110 ZN.9: 2 residues within 4Å: Chain B: D.93 Ligands: ACT.15 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:D.93, B:D.93, ACT.15 ZN.13: 4 residues within 4Å: Chain B: E.35, H.39 Ligands: ACT.5, ACT.14 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Ligand interactions Metal complexes: B:E.35, B:H.39, ACT.5, ACT.14 ZN.16: 3 residues within 4Å: Chain B: H.106, E.110, R.113 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.106, B:E.110

6 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 5 residues within 4Å: Chain A: E.35, H.39 Ligands: ZN.3, ACT.12, ACT.14 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:H.39, A:H.39 ACT.5: 7 residues within 4Å: Chain A: R.38, H.39, A.42 Chain B: E.35, H.39 Ligands: ZN.13, ACT.14 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:R.38 Hydrogen bonds: A:R.38 Water bridges: A:R.128 Salt bridges: A:R.38, A:R.128, B:H.39 ACT.12: 7 residues within 4Å: Chain A: E.35, H.39 Chain B: R.38, H.39, A.42 Ligands: ZN.3, ACT.4 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:R.38 Hydrogen bonds: B:R.38 Water bridges: B:R.128 Salt bridges: B:R.38, A:H.39 ACT.14: 5 residues within 4Å: Chain B: E.35, H.39 Ligands: ACT.4, ACT.5, ZN.13 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:H.39, A:H.39 ACT.15: 4 residues within 4Å: Chain B: D.93, R.95, A.99 Ligands: ZN.9 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.99 Salt bridges: B:R.95 ACT.17: 4 residues within 4Å: Chain B: A.64, H.68, H.91, P.92 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.68, B:H.91

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Daithankar, V.N. et al., Structure of the human sulfhydryl oxidase augmenter of liver regeneration and characterization of a human mutation causing an autosomal recessive myopathy . Biochemistry (2010)

Release Date

2010-07-21

Peptides

FAD-linked sulfhydryl oxidase ALR: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

FAD-linked sulfhydryl oxidase ALR

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