- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.54 Å
- Oligo State
- homo-tetramer
- Ligands
- 5 x NA: SODIUM ION(Non-functional Binders)
- 4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)
NAD.3: 30 residues within 4Å:- Chain A: T.204, T.205, T.206, D.237, N.238, G.267, G.269, D.270, V.271, S.289, E.290, V.291, D.292, C.295, A.322, T.323, G.324, N.325, I.328, I.346, G.347, H.348, L.389, N.391, H.398
- Chain B: L.456, Q.460, K.473, Y.477
- Ligands: ADE.4
27 PLIP interactions:21 interactions with chain A, 6 interactions with chain B- Hydrophobic interactions: A:N.238, A:V.271
- Hydrogen bonds: A:T.205, A:T.205, A:T.205, A:T.206, A:N.238, A:G.269, A:D.270, A:V.271, A:V.291, A:D.292, A:N.325, A:H.348, A:N.391, A:N.391, B:Q.460, B:K.473, B:K.473, B:Y.477, B:Y.477
- Water bridges: A:N.228, A:D.270, A:G.272, A:F.349, A:E.352, B:Q.460
NAD.7: 31 residues within 4Å:- Chain A: L.456, Q.460, K.473, Y.477
- Chain B: T.204, T.205, T.206, D.237, N.238, C.242, G.267, G.269, D.270, V.271, S.289, E.290, V.291, D.292, C.295, A.322, T.323, G.324, N.325, I.328, I.346, G.347, H.348, L.389, N.391, H.398
- Ligands: ADE.8
28 PLIP interactions:23 interactions with chain B, 5 interactions with chain A- Hydrophobic interactions: B:N.238, B:V.271
- Hydrogen bonds: B:T.205, B:T.205, B:T.205, B:T.206, B:T.206, B:N.238, B:G.269, B:D.270, B:V.271, B:V.291, B:D.292, B:N.325, B:I.346, B:H.348, B:N.391, A:Q.460, A:Q.460, A:K.473, A:K.473
- Water bridges: B:N.228, B:D.270, B:G.272, B:S.289, B:F.349, B:E.352, A:R.457
NAD.12: 31 residues within 4Å:- Chain C: T.204, T.205, T.206, D.237, N.238, C.242, G.267, G.269, D.270, V.271, S.289, E.290, V.291, D.292, C.295, A.322, T.323, G.324, N.325, I.328, I.346, G.347, H.348, L.389, N.391, H.398
- Chain D: L.456, Q.460, K.473, Y.477
- Ligands: 3D1.13
25 PLIP interactions:20 interactions with chain C, 5 interactions with chain D- Hydrophobic interactions: C:V.271
- Hydrogen bonds: C:T.205, C:T.205, C:T.205, C:T.206, C:N.238, C:G.269, C:D.270, C:V.271, C:V.291, C:D.292, C:N.325, C:H.348, C:N.391, C:N.391, D:Q.460, D:Q.460, D:K.473, D:K.473, D:Y.477
- Water bridges: C:N.228, C:G.272, C:S.289, C:F.349, C:E.352
NAD.16: 31 residues within 4Å:- Chain C: L.456, Q.460, K.473, Y.477
- Chain D: T.204, T.205, T.206, D.237, N.238, C.242, G.267, G.269, D.270, V.271, S.289, E.290, V.291, D.292, C.295, A.322, T.323, G.324, N.325, I.328, I.346, G.347, H.348, L.389, N.391, H.398
- Ligands: 3D1.17
27 PLIP interactions:22 interactions with chain D, 5 interactions with chain C- Hydrophobic interactions: D:N.238, D:V.271
- Hydrogen bonds: D:T.205, D:T.205, D:T.205, D:T.206, D:T.206, D:N.238, D:G.269, D:D.270, D:V.271, D:V.291, D:D.292, D:N.325, D:H.348, D:N.391, D:N.391, C:Q.460, C:K.473, C:K.473, C:Y.477
- Water bridges: D:N.228, D:G.272, D:S.289, D:G.324, D:F.349, C:Q.460
- 2 x ADE: ADENINE(Non-covalent)
ADE.4: 13 residues within 4Å:- Chain A: L.63, H.64, T.66, Q.68, T.69, L.392, M.396, G.397, H.398, M.403, F.407
- Ligands: NA.1, NAD.3
9 PLIP interactions:9 interactions with chain A- Hydrogen bonds: A:Q.68, A:T.69, A:H.398
- Water bridges: A:D.141, A:E.203, A:D.237, A:D.237, A:D.237, A:H.398
ADE.8: 13 residues within 4Å:- Chain B: L.63, H.64, T.66, Q.68, T.69, L.392, M.396, G.397, H.398, M.403, F.407
- Ligands: NA.6, NAD.7
8 PLIP interactions:8 interactions with chain B- Hydrogen bonds: B:T.66, B:Q.68, B:T.69, B:H.398
- Water bridges: B:D.141, B:D.237, B:D.237, B:H.398
- 3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
PEG.5: 7 residues within 4Å:- Chain A: R.243, E.244, Q.281
- Chain C: R.251, Q.281, A.282, G.283
4 PLIP interactions:1 interactions with chain B, 2 interactions with chain A, 1 interactions with chain C- Water bridges: B:E.302, A:R.243
- Hydrogen bonds: A:R.243, C:R.251
PEG.9: 6 residues within 4Å:- Chain B: D.25, F.26, K.29
- Chain D: I.366, K.367, P.368
1 PLIP interactions:1 interactions with chain B- Water bridges: B:D.25
PEG.18: 7 residues within 4Å:- Chain B: R.251, Q.281, A.282, G.283
- Chain D: R.243, E.244, Q.281
5 PLIP interactions:3 interactions with chain D, 1 interactions with chain C, 1 interactions with chain B- Hydrogen bonds: D:R.243, B:R.251
- Water bridges: D:R.243, D:V.247, C:E.302
- 2 x ACT: ACETATE ION(Non-functional Binders)
ACT.10: 5 residues within 4Å:- Chain B: D.350, I.355, A.356, R.359, R.388
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:I.355
- Salt bridges: B:R.359, B:R.388
ACT.14: 4 residues within 4Å:- Chain C: D.350, I.355, A.356, R.359
3 PLIP interactions:3 interactions with chain C- Hydrophobic interactions: C:I.355
- Water bridges: C:E.169
- Salt bridges: C:R.359
- 2 x 3D1: (2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol(Non-covalent)
3D1.13: 20 residues within 4Å:- Chain C: L.63, H.64, T.66, Q.68, T.69, D.141, E.203, T.204, K.233, D.237, H.348, L.389, L.392, M.396, G.397, H.398, M.403, F.407
- Ligands: NA.11, NAD.12
5 PLIP interactions:5 interactions with chain C- Hydrogen bonds: C:Q.68, C:T.204, C:K.233, C:H.348, C:H.398
3D1.17: 19 residues within 4Å:- Chain D: L.63, H.64, T.66, Q.68, T.69, D.141, E.203, T.204, K.233, D.237, H.348, L.392, M.396, G.397, H.398, M.403, F.407
- Ligands: NA.15, NAD.16
8 PLIP interactions:8 interactions with chain D- Hydrogen bonds: D:T.66, D:Q.68, D:T.204, D:T.204, D:K.233, D:H.348, D:H.398
- Water bridges: D:D.141
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Manszewski, T. et al., Crystallographic and SAXS studies of S-adenosyl-l-homocysteine hydrolase from Bradyrhizobium elkanii. IUCrJ (2017)
- Release Date
- 2017-05-10
- Peptides
- Adenosylhomocysteinase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.54 Å
- Oligo State
- homo-tetramer
- Ligands
- 5 x NA: SODIUM ION(Non-functional Binders)
- 4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)
- 2 x ADE: ADENINE(Non-covalent)
- 3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 2 x ACT: ACETATE ION(Non-functional Binders)
- 2 x 3D1: (2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Manszewski, T. et al., Crystallographic and SAXS studies of S-adenosyl-l-homocysteine hydrolase from Bradyrhizobium elkanii. IUCrJ (2017)
- Release Date
- 2017-05-10
- Peptides
- Adenosylhomocysteinase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D