SMTL ID : 7xrm.1

Ethanolamine ammonia-lyase complexed with AdoMeCbl

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.13 Å

Oligo State

hetero-6-6-mer

Ligands

33 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: R.114, V.143, K.145, R.316, G.356 Ligand excluded by PLIP GOL.2: 4 residues within 4Å: Chain A: K.139, G.155 Chain C: N.420 Ligands: GOL.4 Ligand excluded by PLIP GOL.3: 10 residues within 4Å: Chain A: G.272, A.273, N.276, I.278, G.280, E.281, N.282, C.283 Chain G: N.81, K.115 Ligand excluded by PLIP GOL.4: 7 residues within 4Å: Chain A: L.419, N.420 Chain C: L.418, L.419, N.420 Ligands: GOL.2, GOL.9 Ligand excluded by PLIP GOL.8: 5 residues within 4Å: Chain C: R.114, V.143, K.145, R.316, G.356 Ligand excluded by PLIP GOL.9: 7 residues within 4Å: Chain A: L.419, N.420 Chain C: L.419, N.420 Ligands: GOL.4, GOL.11, GOL.13 Ligand excluded by PLIP GOL.10: 4 residues within 4Å: Chain C: K.139, K.140, P.142, P.154 Ligand excluded by PLIP GOL.11: 7 residues within 4Å: Chain C: P.154, G.155, T.156, N.420, R.422 Ligands: GOL.9, GOL.13 Ligand excluded by PLIP GOL.12: 3 residues within 4Å: Chain C: R.277 Chain I: Q.87, F.112 Ligand excluded by PLIP GOL.13: 4 residues within 4Å: Chain C: N.420, R.422 Ligands: GOL.9, GOL.11 Ligand excluded by PLIP GOL.14: 2 residues within 4Å: Chain C: M.434, L.451 Ligand excluded by PLIP GOL.18: 5 residues within 4Å: Chain E: R.114, V.143, K.145, R.316, G.356 Ligand excluded by PLIP GOL.19: 4 residues within 4Å: Chain E: K.139, G.155 Chain G: N.420 Ligands: GOL.21 Ligand excluded by PLIP GOL.20: 10 residues within 4Å: Chain E: G.272, A.273, N.276, I.278, G.280, E.281, N.282, C.283 Chain K: N.81, K.115 Ligand excluded by PLIP GOL.21: 7 residues within 4Å: Chain E: L.419, N.420 Chain G: L.418, L.419, N.420 Ligands: GOL.19, GOL.26 Ligand excluded by PLIP GOL.25: 5 residues within 4Å: Chain G: R.114, V.143, K.145, R.316, G.356 Ligand excluded by PLIP GOL.26: 7 residues within 4Å: Chain E: L.419, N.420 Chain G: L.419, N.420 Ligands: GOL.21, GOL.28, GOL.30 Ligand excluded by PLIP GOL.27: 4 residues within 4Å: Chain G: K.139, K.140, P.142, P.154 Ligand excluded by PLIP GOL.28: 7 residues within 4Å: Chain G: P.154, G.155, T.156, N.420, R.422 Ligands: GOL.26, GOL.30 Ligand excluded by PLIP GOL.29: 3 residues within 4Å: Chain A: Q.87, F.112 Chain G: R.277 Ligand excluded by PLIP GOL.30: 4 residues within 4Å: Chain G: N.420, R.422 Ligands: GOL.26, GOL.28 Ligand excluded by PLIP GOL.31: 2 residues within 4Å: Chain G: M.434, L.451 Ligand excluded by PLIP GOL.35: 5 residues within 4Å: Chain I: R.114, V.143, K.145, R.316, G.356 Ligand excluded by PLIP GOL.36: 4 residues within 4Å: Chain I: K.139, G.155 Chain K: N.420 Ligands: GOL.38 Ligand excluded by PLIP GOL.37: 10 residues within 4Å: Chain C: N.81, K.115 Chain I: G.272, A.273, N.276, I.278, G.280, E.281, N.282, C.283 Ligand excluded by PLIP GOL.38: 7 residues within 4Å: Chain I: L.419, N.420 Chain K: L.418, L.419, N.420 Ligands: GOL.36, GOL.43 Ligand excluded by PLIP GOL.42: 5 residues within 4Å: Chain K: R.114, V.143, K.145, R.316, G.356 Ligand excluded by PLIP GOL.43: 7 residues within 4Å: Chain I: L.419, N.420 Chain K: L.419, N.420 Ligands: GOL.38, GOL.45, GOL.47 Ligand excluded by PLIP GOL.44: 4 residues within 4Å: Chain K: K.139, K.140, P.142, P.154 Ligand excluded by PLIP GOL.45: 7 residues within 4Å: Chain K: P.154, G.155, T.156, N.420, R.422 Ligands: GOL.43, GOL.47 Ligand excluded by PLIP GOL.46: 3 residues within 4Å: Chain E: Q.87, F.112 Chain K: R.277 Ligand excluded by PLIP GOL.47: 4 residues within 4Å: Chain K: N.420, R.422 Ligands: GOL.43, GOL.45 Ligand excluded by PLIP GOL.48: 2 residues within 4Å: Chain K: M.434, L.451 Ligand excluded by PLIP

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

NH4.5: 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:G.289, A:E.308 Water bridges: A:G.291, A:N.311, A:N.311 NH4.15: 5 residues within 4Å: Chain C: G.289, Q.290, S.292, E.308, N.311 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.292, C:N.311 Water bridges: C:G.291, C:S.292 NH4.22: 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:E.308, E:E.308 Water bridges: E:G.291, E:N.311, E:N.311 NH4.32: 5 residues within 4Å: Chain G: G.289, Q.290, S.292, E.308, N.311 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:G.289, G:N.311 Water bridges: G:G.291, G:S.292 NH4.39: 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 Water bridges: I:G.291, I:N.311, I:N.311 NH4.49: 5 residues within 4Å: Chain K: G.289, Q.290, S.292, E.308, N.311 4 PLIP interactions: 4 interactions with chain K Hydrogen bonds: K:E.308, K:N.311 Water bridges: K:G.291, K:S.292

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.6: 13 residues within 4Å: Chain A: N.193, L.225, F.245, S.247, I.248, E.287, T.288, G.289, S.292, V.326, F.329, I.330 Ligands: B12.7 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.329 Hydrogen bonds: A:N.193, A:S.247, A:S.292, A:S.292, A:S.292 Water bridges: A:G.289, A:G.289, A:F.329 FWK.16: 13 residues within 4Å: Chain C: N.193, L.225, F.245, S.247, I.248, E.287, T.288, G.289, S.292, V.326, F.329, I.330 Ligands: B12.17 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:F.329 Hydrogen bonds: C:N.193, C:S.247, C:E.287, C:S.292, C:S.292 Water bridges: C:R.160, C:G.289, C:G.289, C:F.329 FWK.23: 13 residues within 4Å: Chain E: N.193, L.225, F.245, S.247, I.248, E.287, T.288, G.289, S.292, V.326, F.329, I.330 Ligands: B12.24 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:F.329 Hydrogen bonds: E:N.193, E:S.247, E:S.292, E:S.292, E:S.292 Water bridges: E:G.289, E:G.289, E:F.329 FWK.33: 13 residues within 4Å: Chain G: N.193, L.225, F.245, S.247, I.248, E.287, T.288, G.289, S.292, V.326, F.329, I.330 Ligands: B12.34 10 PLIP interactions: 10 interactions with chain G Hydrophobic interactions: G:F.329 Hydrogen bonds: G:N.193, G:S.247, G:E.287, G:S.292, G:S.292 Water bridges: G:R.160, G:G.289, G:G.289, G:F.329 FWK.40: 13 residues within 4Å: Chain I: N.193, L.225, F.245, S.247, I.248, E.287, T.288, G.289, S.292, V.326, F.329, I.330 Ligands: B12.41 9 PLIP interactions: 9 interactions with chain I Hydrophobic interactions: I:F.329 Hydrogen bonds: I:N.193, I:S.247, I:S.292, I:S.292, I:S.292 Water bridges: I:G.289, I:G.289, I:F.329 FWK.50: 13 residues within 4Å: Chain K: N.193, L.225, F.245, S.247, I.248, E.287, T.288, G.289, S.292, V.326, F.329, I.330 Ligands: B12.51 10 PLIP interactions: 10 interactions with chain K Hydrophobic interactions: K:F.329 Hydrogen bonds: K:N.193, K:S.247, K:E.287, K:S.292, K:S.292 Water bridges: K:R.160, K:G.289, K:G.289, K:F.329

6 x B12: COBALAMIN(Non-covalent)

B12.7: 31 residues within 4Å: Chain A: N.193, P.194, V.195, D.197, A.226, H.227, F.245, Q.246, S.247, E.257, F.258, S.295, F.329, I.330, M.401, L.402 Chain B: R.109, L.137, R.174, V.175, G.195, E.196, R.197, Y.209, E.221, A.222, R.224, C.226, S.228, N.229 Ligands: FWK.6 32 PLIP interactions: 13 interactions with chain A, 18 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: A:F.258, A:F.258, A:F.329, A:L.402, B:L.137, B:Y.209, B:E.221, B:R.224 Hydrogen bonds: A:N.193, A:N.193, A:V.195, A:L.225, A:Q.246, A:S.247, A:E.257, A:S.295, B:V.175, B:E.196, B:R.197, B:Y.209, B:Y.209, B:E.221 Water bridges: A:Y.334, B:R.109, B:R.109, B:R.109, B:R.174, B:R.174, B:E.221, B:C.226 Salt bridges: B:R.174 Metal complexes: B12.7 B12.17: 32 residues within 4Å: Chain C: N.193, P.194, V.195, D.197, A.226, H.227, Q.246, S.247, E.257, F.258, S.295, F.329, I.330, M.401, L.402 Chain D: Y.101, R.109, L.137, R.174, V.175, K.176, G.195, E.196, R.197, S.207, Y.209, E.221, A.222, R.224, C.226, S.228 Ligands: FWK.16 29 PLIP interactions: 12 interactions with chain C, 16 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: 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:S.295, D:R.109, D:V.175, D:E.196, D:R.197, D:S.207, D:Y.209, D:Y.209, D:E.221, D:N.229 Water bridges: C:N.193, D:R.174, D:R.197 Salt bridges: D:R.174 Metal complexes: B12.17 B12.24: 31 residues within 4Å: Chain E: N.193, P.194, V.195, D.197, A.226, H.227, F.245, Q.246, S.247, E.257, F.258, S.295, F.329, I.330, M.401, L.402 Chain F: R.109, L.137, R.174, V.175, G.195, E.196, R.197, Y.209, E.221, A.222, R.224, C.226, S.228, N.229 Ligands: FWK.23 32 PLIP interactions: 13 interactions with chain E, 18 interactions with chain F, 1 Ligand-Ligand interactions Hydrophobic interactions: E:F.258, E:F.258, E:F.329, E:L.402, F:L.137, F:Y.209, F:E.221, F:R.224 Hydrogen bonds: E:N.193, E:N.193, E:V.195, E:L.225, E:Q.246, E:S.247, E:E.257, E:S.295, F:V.175, F:E.196, F:R.197, F:Y.209, F:Y.209, F:E.221 Water bridges: E:Y.334, F:R.109, F:R.109, F:R.109, F:R.174, F:R.174, F:E.221, F:C.226 Salt bridges: F:R.174 Metal complexes: B12.24 B12.34: 32 residues within 4Å: Chain G: N.193, P.194, V.195, D.197, A.226, H.227, Q.246, S.247, E.257, F.258, S.295, F.329, I.330, M.401, L.402 Chain H: Y.101, R.109, L.137, R.174, V.175, K.176, G.195, E.196, R.197, S.207, Y.209, E.221, A.222, R.224, C.226, S.228 Ligands: FWK.33 29 PLIP interactions: 16 interactions with chain H, 12 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.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:E.221, H:N.229, G:P.194, G:V.195, G:D.197, G:Q.246, G:Q.246, G:S.247, G:S.295 Water bridges: H:R.174, H:R.197, G:N.193 Salt bridges: H:R.174 Metal complexes: B12.34 B12.41: 31 residues within 4Å: Chain I: N.193, P.194, V.195, D.197, A.226, H.227, F.245, Q.246, S.247, E.257, F.258, S.295, F.329, I.330, M.401, L.402 Chain J: R.109, L.137, R.174, V.175, G.195, E.196, R.197, Y.209, E.221, A.222, R.224, C.226, S.228, N.229 Ligands: FWK.40 32 PLIP interactions: 13 interactions with chain I, 18 interactions with chain J, 1 Ligand-Ligand interactions Hydrophobic interactions: I:F.258, I:F.258, I:F.329, I:L.402, J:L.137, J:Y.209, J:E.221, J:R.224 Hydrogen bonds: I:N.193, I:N.193, I:V.195, I:L.225, I:Q.246, I:S.247, I:E.257, I:S.295, J:V.175, J:E.196, J:R.197, J:Y.209, J:Y.209, J:E.221 Water bridges: I:Y.334, J:R.109, J:R.109, J:R.109, J:R.174, J:R.174, J:E.221, J:C.226 Salt bridges: J:R.174 Metal complexes: B12.41 B12.51: 32 residues within 4Å: Chain K: N.193, P.194, V.195, D.197, A.226, H.227, Q.246, S.247, E.257, F.258, S.295, F.329, I.330, M.401, L.402 Chain L: Y.101, R.109, L.137, R.174, V.175, K.176, G.195, E.196, R.197, S.207, Y.209, E.221, A.222, R.224, C.226, S.228 Ligands: FWK.50 29 PLIP interactions: 16 interactions with chain L, 12 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.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:E.221, L:N.229, K:P.194, K:V.195, K:D.197, K:Q.246, K:Q.246, K:S.247, K:S.295 Water bridges: L:R.174, L:R.197, K:N.193 Salt bridges: L:R.174 Metal complexes: B12.51

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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