SMTL ID : 3mbg.1 (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: 24 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 Ligands: ZN.3, ACT.10 25 PLIP interactions: 3 interactions with chain B, 22 interactions with chain A Water bridges: B:D.28, B:D.28, B:D.28, A:R.128 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 FAD.12: 24 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 Ligands: ZN.14, ACT.21 27 PLIP interactions: 23 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:W.41, B:W.41, B:W.41, B:L.83 Hydrogen bonds: B:R.33, B:R.38, B:R.38, B:W.41, B:C.105, B:H.108, B:N.112, B:K.114, B:K.114, B:K.117, B:R.128 Water bridges: B:E.34, A:D.28, A:D.28, 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

8 x ZN: ZINC ION(Non-covalent)

ZN.2: 2 residues within 4Å: Chain A: D.93 Ligands: ACT.9 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.93, A:D.93, ACT.9 ZN.3: 3 residues within 4Å: Chain A: E.34 Ligands: FAD.1, ACT.10 4 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:E.34, A:E.34, H2O.4, ACT.10 ZN.4: 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.6: 4 residues within 4Å: Chain A: E.35, H.39 Ligands: ACT.7, ACT.8 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Ligand interactions Metal complexes: A:E.35, A:H.39, ACT.7, ACT.8 ZN.13: 2 residues within 4Å: Chain B: D.93 Ligands: ACT.20 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.93, B:D.93 ZN.14: 3 residues within 4Å: Chain B: E.34 Ligands: FAD.12, ACT.21 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.34, B:E.34, H2O.8 ZN.15: 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 ZN.17: 4 residues within 4Å: Chain B: E.35, H.39 Ligands: ACT.18, ACT.19 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Ligand interactions Metal complexes: B:E.35, B:H.39, ACT.18, ACT.19

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

NA.5: 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.16: 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

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

ACT.7: 7 residues within 4Å: Chain A: E.35, H.39 Chain B: R.38, H.39, A.42 Ligands: ZN.6, ACT.8 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Salt bridges: A:H.39, B:R.38, B:H.39 Hydrophobic interactions: B:A.42 Hydrogen bonds: B:R.38 ACT.8: 5 residues within 4Å: Chain A: E.35, H.39 Ligands: ZN.6, ACT.7, ACT.19 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:H.39, B:H.39 ACT.9: 5 residues within 4Å: Chain A: D.93, R.95, T.96, A.99 Ligands: ZN.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.95, A:T.96, A:A.99 Salt bridges: A:R.95 ACT.10: 5 residues within 4Å: Chain A: E.34, L.115, K.117 Ligands: FAD.1, ZN.3 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.117 ACT.11: 4 residues within 4Å: Chain A: A.64, H.68, H.91, P.92 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.68, A:H.91 ACT.18: 7 residues within 4Å: Chain A: R.38, H.39, A.42 Chain B: E.35, H.39 Ligands: ZN.17, ACT.19 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:A.42 Hydrogen bonds: A:R.38 Salt bridges: A:R.38, A:H.39, B:H.39 ACT.19: 5 residues within 4Å: Chain B: E.35, H.39 Ligands: ACT.8, ZN.17, ACT.18 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:H.39, B:H.39 ACT.20: 5 residues within 4Å: Chain B: D.93, R.95, T.96, A.99 Ligands: ZN.13 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:R.95, B:T.96, B:A.99 Salt bridges: B:R.95 ACT.21: 5 residues within 4Å: Chain B: E.34, L.115, K.117 Ligands: FAD.12, ZN.14 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.117 ACT.22: 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
A

B
A

FAD-linked sulfhydryl oxidase ALR

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