SMTL ID : 7xrn.1

Ethanolamine ammonia-lyase complexed with AdoMeCbl in the presence of substrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

hetero-6-6-mer

Ligands

6 x FWK: (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-ethyl-oxolane-3,4-diol(Non-covalent)

FWK.1: 11 residues within 4Å: Chain A: N.193, L.225, F.245, S.247, E.287, T.288, G.289, S.292, V.326, F.329 Ligands: B12.5 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.193, A:S.247, A:S.292 Water bridges: A:R.160, A:G.289, A:G.289, A:I.330 FWK.7: 11 residues within 4Å: Chain C: N.193, L.225, F.245, S.247, E.287, T.288, G.289, S.292, V.326, F.329 Ligands: B12.12 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:F.329 Hydrogen bonds: C:N.193, C:S.247, C:S.247, C:S.292 Water bridges: C:R.160, C:S.292, C:S.292, C:F.329 FWK.13: 11 residues within 4Å: Chain E: N.193, L.225, F.245, S.247, E.287, T.288, G.289, S.292, V.326, F.329 Ligands: B12.17 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:N.193, E:S.247, E:S.292 Water bridges: E:R.160, E:G.289, E:G.289, E:I.330 FWK.19: 11 residues within 4Å: Chain G: N.193, L.225, F.245, S.247, E.287, T.288, G.289, S.292, V.326, F.329 Ligands: B12.24 9 PLIP interactions: 9 interactions with chain G Hydrophobic interactions: G:F.329 Hydrogen bonds: G:N.193, G:S.247, G:S.247, G:S.292 Water bridges: G:R.160, G:S.292, G:S.292, G:F.329 FWK.25: 11 residues within 4Å: Chain I: N.193, L.225, F.245, S.247, E.287, T.288, G.289, S.292, V.326, F.329 Ligands: B12.29 7 PLIP interactions: 7 interactions with chain I Hydrogen bonds: I:N.193, I:S.247, I:S.292 Water bridges: I:R.160, I:G.289, I:G.289, I:I.330 FWK.31: 11 residues within 4Å: Chain K: N.193, L.225, F.245, S.247, E.287, T.288, G.289, S.292, V.326, F.329 Ligands: B12.36 9 PLIP interactions: 9 interactions with chain K Hydrophobic interactions: K:F.329 Hydrogen bonds: K:N.193, K:S.247, K:S.247, K:S.292 Water bridges: K:R.160, K:S.292, K:S.292, K:F.329

18 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: D.108 Chain G: P.425, E.426, R.429 Ligand excluded by PLIP GOL.3: 3 residues within 4Å: Chain A: R.316, H.317 Chain G: E.281 Ligand excluded by PLIP GOL.6: 9 residues within 4Å: Chain A: K.444, A.446, G.447, D.448 Chain B: G.25, V.26, E.27, G.49, R.50 Ligand excluded by PLIP GOL.8: 3 residues within 4Å: Chain A: L.419 Chain C: L.419, N.420 Ligand excluded by PLIP GOL.9: 9 residues within 4Å: Chain C: G.272, A.273, I.278, G.280, E.281, N.282, C.283 Chain I: N.81, K.115 Ligand excluded by PLIP GOL.10: 8 residues within 4Å: Chain C: K.115 Chain I: G.272, A.273, I.278, G.280, E.281, N.282, C.283 Ligand excluded by PLIP GOL.14: 4 residues within 4Å: Chain E: D.108 Chain K: P.425, E.426, R.429 Ligand excluded by PLIP GOL.15: 3 residues within 4Å: Chain E: R.316, H.317 Chain K: E.281 Ligand excluded by PLIP GOL.18: 9 residues within 4Å: Chain E: K.444, A.446, G.447, D.448 Chain F: G.25, V.26, E.27, G.49, R.50 Ligand excluded by PLIP GOL.20: 3 residues within 4Å: Chain E: L.419 Chain G: L.419, N.420 Ligand excluded by PLIP GOL.21: 9 residues within 4Å: Chain A: N.81, K.115 Chain G: G.272, A.273, I.278, G.280, E.281, N.282, C.283 Ligand excluded by PLIP GOL.22: 8 residues within 4Å: Chain A: G.272, A.273, I.278, G.280, E.281, N.282, C.283 Chain G: K.115 Ligand excluded by PLIP GOL.26: 4 residues within 4Å: Chain C: P.425, E.426, R.429 Chain I: D.108 Ligand excluded by PLIP GOL.27: 3 residues within 4Å: Chain C: E.281 Chain I: R.316, H.317 Ligand excluded by PLIP GOL.30: 9 residues within 4Å: Chain I: K.444, A.446, G.447, D.448 Chain J: G.25, V.26, E.27, G.49, R.50 Ligand excluded by PLIP GOL.32: 3 residues within 4Å: Chain I: L.419 Chain K: L.419, N.420 Ligand excluded by PLIP GOL.33: 9 residues within 4Å: Chain E: N.81, K.115 Chain K: G.272, A.273, I.278, G.280, E.281, N.282, C.283 Ligand excluded by PLIP GOL.34: 8 residues within 4Å: Chain E: G.272, A.273, I.278, G.280, E.281, N.282, C.283 Chain K: K.115 Ligand excluded by PLIP

6 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.4: 4 residues within 4Å: Chain A: G.289, S.292, E.308, N.311 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.308, A:E.308, A:N.311 Water bridges: A:G.289, A:G.291 NH4.11: 4 residues within 4Å: Chain C: G.289, S.292, E.308, N.311 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:M.307, C:N.311 Water bridges: C:G.291, C:S.292 NH4.16: 4 residues within 4Å: Chain E: G.289, S.292, E.308, N.311 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:G.289, E:E.308, E:N.311 Water bridges: E:G.289, E:G.291 NH4.23: 4 residues within 4Å: Chain G: G.289, S.292, E.308, N.311 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:M.307, G:N.311 Water bridges: G:G.291, G:S.292 NH4.28: 4 residues within 4Å: Chain I: G.289, S.292, E.308, N.311 5 PLIP interactions: 5 interactions with chain I Hydrogen bonds: I:E.308, I:E.308, I:N.311 Water bridges: I:G.289, I:G.291 NH4.35: 4 residues within 4Å: Chain K: G.289, S.292, E.308, N.311 4 PLIP interactions: 4 interactions with chain K Hydrogen bonds: K:G.289, K:N.311 Water bridges: K:G.291, K:S.292

6 x B12: COBALAMIN(Non-covalent)

B12.5: 36 residues within 4Å: Chain A: N.193, P.194, V.195, T.196, D.197, L.225, A.226, H.227, F.245, Q.246, S.247, E.257, F.258, S.295, F.329, I.330, M.401, L.402, N.403 Chain B: Y.101, R.109, L.137, R.174, V.175, K.176, E.196, R.197, S.207, Y.209, E.221, A.222, R.224, C.226, S.228, N.229 Ligands: FWK.1 36 PLIP interactions: 19 interactions with chain B, 16 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: B:L.137, B:Y.209, B:E.221, B:R.224, A:F.258, A:F.258, A:F.329, A:F.329, A:L.402 Hydrogen bonds: B:R.109, B:V.175, B:K.176, B:K.176, B:E.196, B:R.197, B:S.207, B:Y.209, B:Y.209, A:P.194, A:V.195, A:L.225, A:Q.246, A:S.247, A:E.257, A:S.295, A:S.295 Water bridges: B:R.174, B:R.174, B:R.174, B:K.176, B:S.228, A:N.193, A:N.193, A:Y.334 Salt bridges: B:R.174 Metal complexes: B12.5 B12.12: 34 residues within 4Å: Chain C: N.193, P.194, V.195, L.225, A.226, H.227, F.245, Q.246, S.247, E.257, F.258, S.295, F.329, I.330, M.401, L.402, N.403 Chain D: Y.101, R.109, L.137, R.174, V.175, K.176, G.195, E.196, R.197, Y.209, E.221, A.222, R.224, C.226, S.228, N.229 Ligands: FWK.7 41 PLIP interactions: 17 interactions with chain C, 23 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: C:F.258, C:F.258, C:F.329, C:I.330, C:L.402, D:L.137, D:Y.209, D:E.221, D:R.224 Hydrogen bonds: C:P.194, C:V.195, C:D.197, C:Q.246, C:Q.246, C:S.247, C:E.257, C:S.295, C:S.295, D:R.109, D:V.175, D:E.196, D:R.197, D:S.207, D:Y.209, D:Y.209, D:S.228 Water bridges: C:N.193, C:N.193, C:E.333, D:R.174, D:R.174, D:R.174, D:R.174, D:K.176, D:K.176, D:R.197, D:C.226, D:C.226, D:S.228 Salt bridges: D:R.174 Metal complexes: B12.12 B12.17: 36 residues within 4Å: Chain E: N.193, P.194, V.195, T.196, D.197, L.225, A.226, H.227, F.245, Q.246, S.247, E.257, F.258, S.295, F.329, I.330, M.401, L.402, N.403 Chain F: Y.101, R.109, L.137, R.174, V.175, K.176, E.196, R.197, S.207, Y.209, E.221, A.222, R.224, C.226, S.228, N.229 Ligands: FWK.13 36 PLIP interactions: 16 interactions with chain E, 19 interactions with chain F, 1 Ligand-Ligand interactions Hydrophobic interactions: E:F.258, E:F.258, E:F.329, E:F.329, E:L.402, F:L.137, F:Y.209, F:E.221, F:R.224 Hydrogen bonds: E:P.194, E:V.195, E:L.225, E:Q.246, E:S.247, E:E.257, E:S.295, E:S.295, F:R.109, F:V.175, F:K.176, F:K.176, F:E.196, F:R.197, F:S.207, F:Y.209, F:Y.209 Water bridges: E:N.193, E:N.193, E:Y.334, F:R.174, F:R.174, F:R.174, F:K.176, F:S.228 Salt bridges: F:R.174 Metal complexes: B12.17 B12.24: 34 residues within 4Å: Chain G: N.193, P.194, V.195, L.225, A.226, H.227, F.245, Q.246, S.247, E.257, F.258, S.295, F.329, I.330, M.401, L.402, N.403 Chain H: Y.101, R.109, L.137, R.174, V.175, K.176, G.195, E.196, R.197, Y.209, E.221, A.222, R.224, C.226, S.228, N.229 Ligands: FWK.19 41 PLIP interactions: 23 interactions with chain H, 17 interactions with chain G, 1 Ligand-Ligand interactions Hydrophobic interactions: H:L.137, H:Y.209, H:E.221, H:R.224, G:F.258, G:F.258, G:F.329, G:I.330, G:L.402 Hydrogen bonds: H:R.109, H:V.175, H:E.196, H:R.197, H:S.207, H:Y.209, H:Y.209, H:S.228, G:P.194, G:V.195, G:D.197, G:Q.246, G:Q.246, G:S.247, G:E.257, G:S.295, G:S.295 Water bridges: H:R.174, H:R.174, H:R.174, H:R.174, H:K.176, H:K.176, H:R.197, H:C.226, H:C.226, H:S.228, G:N.193, G:N.193, G:E.333 Salt bridges: H:R.174 Metal complexes: B12.24 B12.29: 36 residues within 4Å: Chain I: N.193, P.194, V.195, T.196, D.197, L.225, A.226, H.227, F.245, Q.246, S.247, E.257, F.258, S.295, F.329, I.330, M.401, L.402, N.403 Chain J: Y.101, R.109, L.137, R.174, V.175, K.176, E.196, R.197, S.207, Y.209, E.221, A.222, R.224, C.226, S.228, N.229 Ligands: FWK.25 36 PLIP interactions: 19 interactions with chain J, 16 interactions with chain I, 1 Ligand-Ligand interactions Hydrophobic interactions: J:L.137, J:Y.209, J:E.221, J:R.224, I:F.258, I:F.258, I:F.329, I:F.329, I:L.402 Hydrogen bonds: J:R.109, J:V.175, J:K.176, J:K.176, J:E.196, J:R.197, J:S.207, J:Y.209, J:Y.209, I:P.194, I:V.195, I:L.225, I:Q.246, I:S.247, I:E.257, I:S.295, I:S.295 Water bridges: J:R.174, J:R.174, J:R.174, J:K.176, J:S.228, I:N.193, I:N.193, I:Y.334 Salt bridges: J:R.174 Metal complexes: B12.29 B12.36: 34 residues within 4Å: Chain K: N.193, P.194, V.195, L.225, A.226, H.227, F.245, Q.246, S.247, E.257, F.258, S.295, F.329, I.330, M.401, L.402, N.403 Chain L: Y.101, R.109, L.137, R.174, V.175, K.176, G.195, E.196, R.197, Y.209, E.221, A.222, R.224, C.226, S.228, N.229 Ligands: FWK.31 41 PLIP interactions: 23 interactions with chain L, 17 interactions with chain K, 1 Ligand-Ligand interactions Hydrophobic interactions: L:L.137, L:Y.209, L:E.221, L:R.224, K:F.258, K:F.258, K:F.329, K:I.330, K:L.402 Hydrogen bonds: L:R.109, L:V.175, L:E.196, L:R.197, L:S.207, L:Y.209, L:Y.209, L:S.228, K:P.194, K:V.195, K:D.197, K:Q.246, K:Q.246, K:S.247, K:E.257, K:S.295, K:S.295 Water bridges: L:R.174, L:R.174, L:R.174, L:R.174, L:K.176, L:K.176, L:R.197, L:C.226, L:C.226, L:S.228, K:N.193, K:N.193, K:E.333 Salt bridges: L:R.174 Metal complexes: B12.36

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shibata, N. et al., Structural Insights into the Very Low Activity of the Homocoenzyme B 12 Adenosylmethylcobalamin in Coenzyme B 12 -Dependent Diol Dehydratase and Ethanolamine Ammonia-Lyase. Chemistry (2022)

Release Date

2023-03-29

Peptides

Ethanolamine ammonia-lyase large subunit: ACEGIK
Ethanolamine ammonia-lyase small subunit: BDFHJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
A

G
C

I
A

K
C

B
B

D
D

F
B

H
D

J
B

L
D

Ethanolamine ammonia-lyase large subunit

Ethanolamine ammonia-lyase small subunit

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