SMTL ID : 6aph.1

Crystal structure of Adenosylhomocysteinase from Elizabethkingia anophelis NUHP1 in complex with NAD and Adenosine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 30 residues within 4Å: Chain A: T.170, T.171, T.172, D.203, N.204, G.233, G.235, D.236, V.237, T.255, E.256, I.257, D.258, C.261, T.288, T.289, G.290, N.291, I.294, I.312, G.313, H.314, L.357, N.359, H.366 Chain C: E.420, Q.426, K.439, Y.443 Ligands: ADN.2 28 PLIP interactions: 5 interactions with chain C, 23 interactions with chain A Hydrogen bonds: C:Q.426, C:K.439, C:K.439, C:Y.443, A:T.171, A:T.171, A:T.172, A:T.172, A:T.172, A:N.204, A:D.236, A:V.237, A:T.255, A:I.257, A:D.258, A:N.291, A:H.314, A:N.359, A:N.359 Water bridges: C:Q.426, A:G.235, A:D.236, A:D.236, A:G.238, A:F.315, A:E.318 Hydrophobic interactions: A:N.204, A:V.237 NAD.4: 30 residues within 4Å: Chain B: T.170, T.171, T.172, D.203, N.204, G.233, G.235, D.236, V.237, T.255, E.256, I.257, D.258, C.261, T.288, T.289, G.290, N.291, I.294, I.312, G.313, H.314, L.357, N.359, H.366 Chain D: E.420, Q.426, K.439, Y.443 Ligands: ADN.5 28 PLIP interactions: 23 interactions with chain B, 5 interactions with chain D Hydrophobic interactions: B:N.204, B:V.237 Hydrogen bonds: B:T.171, B:T.171, B:T.172, B:T.172, B:T.172, B:N.204, B:D.236, B:V.237, B:T.255, B:I.257, B:D.258, B:N.291, B:H.314, B:N.359, B:N.359, D:Q.426, D:K.439, D:K.439, D:Y.443 Water bridges: B:G.235, B:D.236, B:D.236, B:G.238, B:F.315, B:E.318, D:Q.426 NAD.7: 30 residues within 4Å: Chain A: E.420, Q.426, K.439, Y.443 Chain C: T.170, T.171, T.172, D.203, N.204, G.233, G.235, D.236, V.237, T.255, E.256, I.257, D.258, C.261, T.288, T.289, G.290, N.291, I.294, I.312, G.313, H.314, L.357, N.359, H.366 Ligands: ADN.8 26 PLIP interactions: 20 interactions with chain C, 6 interactions with chain A Hydrophobic interactions: C:N.204, C:V.237 Hydrogen bonds: C:T.171, C:T.172, C:T.172, C:N.204, C:D.236, C:V.237, C:I.257, C:D.258, C:N.291, C:H.314, C:N.359, C:N.359, A:Q.426, A:K.439, A:K.439, A:Y.443, A:Y.443 Water bridges: C:N.194, C:G.235, C:G.238, C:T.255, C:F.315, C:E.318, A:Q.426 NAD.10: 30 residues within 4Å: Chain B: E.420, Q.426, K.439, Y.443 Chain D: T.170, T.171, T.172, D.203, N.204, G.233, G.235, D.236, V.237, T.255, E.256, I.257, D.258, C.261, T.288, T.289, G.290, N.291, I.294, I.312, G.313, H.314, L.357, N.359, H.366 Ligands: ADN.11 26 PLIP interactions: 20 interactions with chain D, 6 interactions with chain B Hydrophobic interactions: D:N.204, D:V.237 Hydrogen bonds: D:T.171, D:T.172, D:T.172, D:N.204, D:D.236, D:V.237, D:I.257, D:D.258, D:N.291, D:H.314, D:N.359, D:N.359, B:Q.426, B:K.439, B:K.439, B:Y.443, B:Y.443 Water bridges: D:N.194, D:G.235, D:G.238, D:T.255, D:F.315, D:E.318, B:Q.426

4 x ADN: ADENOSINE(Non-covalent)

ADN.2: 19 residues within 4Å: Chain A: L.65, H.66, T.68, Q.70, T.71, D.144, E.169, T.170, K.199, D.203, H.314, L.357, L.360, T.364, G.365, H.366, M.371, F.375 Ligands: NAD.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:T.68, A:Q.70, A:T.71, A:T.170, A:T.170, A:K.199, A:K.199, A:H.314, A:H.366 ADN.5: 19 residues within 4Å: Chain B: L.65, H.66, T.68, Q.70, T.71, D.144, E.169, T.170, K.199, D.203, H.314, L.357, L.360, T.364, G.365, H.366, M.371, F.375 Ligands: NAD.4 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:T.68, B:Q.70, B:T.71, B:T.170, B:T.170, B:K.199, B:K.199, B:H.314, B:H.366 ADN.8: 19 residues within 4Å: Chain C: L.65, H.66, T.68, Q.70, T.71, D.144, E.169, T.170, K.199, D.203, H.314, L.357, L.360, T.364, G.365, H.366, M.371, F.375 Ligands: NAD.7 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Q.70, C:E.169, C:T.170, C:K.199, C:K.199, C:H.314, C:H.366 ADN.11: 19 residues within 4Å: Chain D: L.65, H.66, T.68, Q.70, T.71, D.144, E.169, T.170, K.199, D.203, H.314, L.357, L.360, T.364, G.365, H.366, M.371, F.375 Ligands: NAD.10 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:Q.70, D:E.169, D:T.170, D:K.199, D:K.199, D:H.314, D:H.366

4 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 3 residues within 4Å: Chain A: E.425, K.428, Y.429 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.429 Hydrogen bonds: A:E.425 MPD.6: 3 residues within 4Å: Chain B: E.425, K.428, Y.429 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.429 Hydrogen bonds: B:E.425 MPD.9: 3 residues within 4Å: Chain C: E.425, K.428, Y.429 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.429 Hydrogen bonds: C:E.425 MPD.12: 3 residues within 4Å: Chain D: E.425, K.428, Y.429 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:Y.429 Hydrogen bonds: D:E.425

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abendroth, J. et al., Crystal structure of Adenosylhomocysteinase from Elizabethkingia anophelis NUHP1 in complex with NAD and Adenosine. To be Published

Release Date

2017-08-30

Peptides

Adenosylhomocysteinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Adenosylhomocysteinase