SMTL ID : 5m5k.1

S-adenosyl-L-homocysteine hydrolase from Bradyrhizobium elkanii in complex with adenosine and cordycepin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

homo-tetramer

Ligands

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 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: ADN.2 25 PLIP interactions: 18 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:N.238, A:V.271 Hydrogen bonds: A:T.205, A:T.206, 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:N.391, A:N.391, B:Q.460, B:K.473, B:K.473, B:Y.477, B:Y.477 Water bridges: A:T.206, A:N.228, A:D.270, A:G.272, B:T.454, B:Q.460 NAD.5: 30 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, 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: ADN.6 25 PLIP interactions: 20 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:N.238, B:G.269, B:D.270, B:V.271, B:V.291, B:D.292, B:N.391, B:N.391, A:Q.460, A:K.473, A:K.473, A:Y.477 Water bridges: B:T.206, B:T.206, B:N.228, B:D.270, B:G.272, B:S.289, A:Q.460 NAD.9: 31 residues within 4Å: Chain C: 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 D: L.456, Q.460, I.464, K.473, Y.477 Ligands: ADN.10 23 PLIP interactions: 16 interactions with chain C, 7 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:N.391, C:H.398, D:Q.460, D:K.473, D:K.473, D:Y.477, D:Y.477 Water bridges: C:N.228, C:G.272, D:T.454, D:Q.460 NAD.12: 27 residues within 4Å: Chain C: L.456, Q.460, K.473, Y.477 Chain D: 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 Ligands: 3AD.13 23 PLIP interactions: 18 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:V.271 Hydrogen bonds: D:G.269, D:D.270, D:V.271, D:V.291, D:D.292, D:N.325, D:N.391, D:N.391, C:Q.460, C:K.473, C:K.473, C:Y.477 Water bridges: D:T.205, D:T.205, D:T.205, D:T.205, D:N.238, D:N.238, D:G.272, D:S.289, D:F.349, C:Q.460

3 x ADN: ADENOSINE(Non-covalent)

ADN.2: 19 residues within 4Å: Chain A: L.63, H.64, T.66, Q.68, T.69, D.141, E.203, T.204, K.233, D.237, L.389, L.392, M.396, G.397, H.398, M.403, F.407 Ligands: NAD.1, NA.3 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:H.64, A:Q.68, A:T.69, A:T.204, A:K.233, A:K.233, A:H.398 Water bridges: A:D.141, A:D.141, A:D.141 ADN.6: 19 residues within 4Å: Chain B: L.63, H.64, T.66, Q.68, T.69, D.141, E.203, T.204, K.233, D.237, L.389, L.392, M.396, G.397, H.398, M.403, F.407 Ligands: NAD.5, NA.7 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:H.64, B:T.66, B:Q.68, B:T.69, B:K.233, B:K.233, B:H.398 Water bridges: B:D.141, B:D.141, B:D.141 ADN.10: 18 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, L.389, L.392, M.396, G.397, H.398, M.403, F.407 Ligands: NAD.9 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Q.68, C:E.203, C:T.204, C:K.233, C:K.233, C:H.398 Water bridges: C:D.141

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

NA.3: 6 residues within 4Å: Chain A: Q.68, M.396, G.397, H.398, P.399 Ligands: ADN.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.398 Water bridges: A:Q.94 NA.7: 6 residues within 4Å: Chain B: Q.68, M.396, G.397, H.398, P.399 Ligands: ADN.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.68 Water bridges: B:Q.94 NA.11: 5 residues within 4Å: Chain C: Q.68, M.396, G.397, H.398, P.399 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:M.396 Water bridges: C:Q.94

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 3 residues within 4Å: Chain A: R.280 Chain B: R.280, Q.281 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.281, B:R.280 Water bridges: A:R.280, A:R.280 PEG.8: 6 residues within 4Å: Chain A: H.209 Chain B: G.465, V.466, P.471, K.473, S.474 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.209

1 x 3AD: 3'-DEOXYADENOSINE(Non-covalent)

3AD.13: 14 residues within 4Å: Chain D: H.64, T.66, Q.68, T.69, D.237, F.349, L.389, L.392, M.396, G.397, H.398, M.403, F.407 Ligands: NAD.12 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:T.66, D:Q.68, D:D.237, D:H.398, D:H.398 Water bridges: D:Q.94, D:E.203

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.14: 4 residues within 4Å: Chain C: G.465, P.471, K.473, S.474 No protein-ligand interaction detected (PLIP)

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

ACT.15: 3 residues within 4Å: Chain D: N.360, L.361, K.362 No protein-ligand interaction detected (PLIP)

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
A

B
B

C
C

D
D

Adenosylhomocysteinase

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