- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.05 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x SIB: (2S)-2-AMINO-4-({[(2S,3S,4R,5R)-3,4-DIHYDROXY-5-(6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)TETRAHYDROFURAN-2-YL]METHYL}THIO)BUTANOIC ACID(Non-covalent)
SIB.1: 22 residues within 4Å:- Chain A: H.75, E.77, K.79, T.80, S.99, N.100, D.148, E.173, T.174, K.203, D.207, G.317, H.318, F.319, L.361, L.364, D.368, G.369, H.370, M.375, F.379
- Ligands: NAD.2
11 PLIP interactions:11 interactions with chain A- Hydrogen bonds: A:E.77, A:K.79, A:N.100, A:D.148, A:T.174, A:K.203, A:K.203, A:F.319, A:H.370
- Water bridges: A:H.75
- Salt bridges: A:H.75
SIB.3: 22 residues within 4Å:- Chain B: H.75, E.77, K.79, T.80, S.99, N.100, D.148, G.149, E.173, T.174, K.203, D.207, H.318, F.319, L.361, L.364, D.368, G.369, H.370, M.375, F.379
- Ligands: NAD.4
18 PLIP interactions:18 interactions with chain B- Hydrophobic interactions: B:H.318
- Hydrogen bonds: B:E.77, B:K.79, B:T.80, B:N.100, B:D.148, B:D.148, B:D.148, B:E.173, B:T.174, B:T.174, B:K.203, B:K.203, B:F.319, B:H.370
- Water bridges: B:H.75, B:Y.130
- Salt bridges: B:H.75
SIB.5: 22 residues within 4Å:- Chain C: H.75, E.77, K.79, T.80, S.99, N.100, D.148, E.173, T.174, K.203, D.207, G.317, H.318, F.319, L.361, L.364, D.368, G.369, H.370, M.375, F.379
- Ligands: NAD.6
11 PLIP interactions:11 interactions with chain C- Hydrogen bonds: C:E.77, C:K.79, C:N.100, C:D.148, C:T.174, C:K.203, C:K.203, C:F.319, C:H.370
- Water bridges: C:H.75
- Salt bridges: C:H.75
SIB.7: 22 residues within 4Å:- Chain D: H.75, E.77, K.79, T.80, S.99, N.100, D.148, G.149, E.173, T.174, K.203, D.207, H.318, F.319, L.361, L.364, D.368, G.369, H.370, M.375, F.379
- Ligands: NAD.8
18 PLIP interactions:18 interactions with chain D- Hydrophobic interactions: D:H.318
- Hydrogen bonds: D:E.77, D:K.79, D:T.80, D:N.100, D:D.148, D:D.148, D:D.148, D:E.173, D:T.174, D:T.174, D:K.203, D:K.203, D:F.319, D:H.370
- Water bridges: D:H.75, D:Y.130
- Salt bridges: D:H.75
- 4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)
NAD.2: 29 residues within 4Å:- Chain A: T.174, T.175, T.176, D.207, N.208, T.212, V.236, G.237, G.239, W.240, C.241, V.259, E.260, V.261, D.262, K.265, A.292, T.293, G.294, N.295, C.298, A.316, G.317, H.318, N.363, H.370
- Chain D: L.426, Q.430
- Ligands: SIB.1
22 PLIP interactions:19 interactions with chain A, 3 interactions with chain D- Hydrogen bonds: A:T.175, A:T.175, A:T.176, A:N.208, A:W.240, A:C.241, A:V.261, A:D.262, A:K.265, A:N.295, A:H.318, A:N.363, A:N.363, D:Q.430, D:Q.430
- Water bridges: A:G.239, A:W.240, A:G.242, A:K.265, A:K.265, D:E.424
- Salt bridges: A:K.265
NAD.4: 30 residues within 4Å:- Chain B: T.174, T.175, T.176, D.207, N.208, T.212, V.236, G.237, G.239, W.240, C.241, V.259, E.260, V.261, D.262, K.265, A.292, T.293, G.294, N.295, C.298, A.316, G.317, H.318, L.361, N.363, H.370
- Chain C: L.426, Q.430
- Ligands: SIB.3
24 PLIP interactions:22 interactions with chain B, 2 interactions with chain C- Hydrogen bonds: B:T.175, B:T.176, B:T.176, B:T.176, B:N.208, B:W.240, B:C.241, B:V.261, B:D.262, B:K.265, B:K.265, B:N.295, B:H.318, B:N.363, B:N.363, C:Q.430, C:Q.430
- Water bridges: B:G.239, B:W.240, B:G.242, B:D.262, B:K.265, B:K.265
- Salt bridges: B:K.265
NAD.6: 29 residues within 4Å:- Chain B: L.426, Q.430
- Chain C: T.174, T.175, T.176, D.207, N.208, T.212, V.236, G.237, G.239, W.240, C.241, V.259, E.260, V.261, D.262, K.265, A.292, T.293, G.294, N.295, C.298, A.316, G.317, H.318, N.363, H.370
- Ligands: SIB.5
22 PLIP interactions:3 interactions with chain B, 19 interactions with chain C- Hydrogen bonds: B:Q.430, B:Q.430, C:T.175, C:T.175, C:T.176, C:N.208, C:W.240, C:C.241, C:V.261, C:D.262, C:K.265, C:N.295, C:H.318, C:N.363, C:N.363
- Water bridges: B:E.424, C:G.239, C:W.240, C:G.242, C:K.265, C:K.265
- Salt bridges: C:K.265
NAD.8: 30 residues within 4Å:- Chain A: L.426, Q.430
- Chain D: T.174, T.175, T.176, D.207, N.208, T.212, V.236, G.237, G.239, W.240, C.241, V.259, E.260, V.261, D.262, K.265, A.292, T.293, G.294, N.295, C.298, A.316, G.317, H.318, L.361, N.363, H.370
- Ligands: SIB.7
24 PLIP interactions:22 interactions with chain D, 2 interactions with chain A- Hydrogen bonds: D:T.175, D:T.176, D:T.176, D:T.176, D:N.208, D:W.240, D:C.241, D:V.261, D:D.262, D:K.265, D:K.265, D:N.295, D:H.318, D:N.363, D:N.363, A:Q.430, A:Q.430
- Water bridges: D:G.239, D:W.240, D:G.242, D:D.262, D:K.265, D:K.265
- Salt bridges: D:K.265
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Saleem-Batcha, R. et al., Crystal structure of S-adenosyl-L-homocysteine hydrolase from Pyrococcus furiosus in complex with S-inosyl-L-homocysteine. To Be Published
- Release Date
- 2023-02-15
- Peptides
- Adenosylhomocysteinase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
AD
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.05 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x SIB: (2S)-2-AMINO-4-({[(2S,3S,4R,5R)-3,4-DIHYDROXY-5-(6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)TETRAHYDROFURAN-2-YL]METHYL}THIO)BUTANOIC ACID(Non-covalent)
- 4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Saleem-Batcha, R. et al., Crystal structure of S-adenosyl-L-homocysteine hydrolase from Pyrococcus furiosus in complex with S-inosyl-L-homocysteine. To Be Published
- Release Date
- 2023-02-15
- Peptides
- Adenosylhomocysteinase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
AD
B