SMTL ID : 5ysn.1

Ethanolamine ammonia-lyase, AdoCbl/substrate-free

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-6-6-mer

Ligands

6 x 5AD: 5'-DEOXYADENOSINE(Non-covalent)

5AD.1: 12 residues within 4Å: Chain A: N.193, F.245, S.247, I.248, E.287, T.288, G.289, S.292, V.326, F.329, I.330 Ligands: B12.8 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.329 Hydrogen bonds: A:N.193, A:S.247, A:E.287, A:G.289 Water bridges: A:S.292, A:S.292, A:F.329 5AD.9: 12 residues within 4Å: Chain C: N.193, F.245, S.247, I.248, E.287, T.288, G.289, S.292, V.326, F.329, I.330 Ligands: B12.15 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.329 Hydrogen bonds: C:N.193, C:S.247, C:G.289 Water bridges: C:G.289, C:F.329 5AD.16: 12 residues within 4Å: Chain E: N.193, F.245, S.247, I.248, E.287, T.288, G.289, S.292, V.326, F.329, I.330 Ligands: B12.23 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:F.329 Hydrogen bonds: E:N.193, E:S.247, E:E.287, E:G.289 Water bridges: E:S.292, E:S.292, E:F.329 5AD.24: 12 residues within 4Å: Chain G: N.193, F.245, S.247, I.248, E.287, T.288, G.289, S.292, V.326, F.329, I.330 Ligands: B12.30 6 PLIP interactions: 6 interactions with chain G Hydrophobic interactions: G:F.329 Hydrogen bonds: G:N.193, G:S.247, G:G.289 Water bridges: G:G.289, G:F.329 5AD.31: 12 residues within 4Å: Chain I: N.193, F.245, S.247, I.248, E.287, T.288, G.289, S.292, V.326, F.329, I.330 Ligands: B12.38 8 PLIP interactions: 8 interactions with chain I Hydrophobic interactions: I:F.329 Hydrogen bonds: I:N.193, I:S.247, I:E.287, I:G.289 Water bridges: I:S.292, I:S.292, I:F.329 5AD.39: 12 residues within 4Å: Chain K: N.193, F.245, S.247, I.248, E.287, T.288, G.289, S.292, V.326, F.329, I.330 Ligands: B12.45 6 PLIP interactions: 6 interactions with chain K Hydrophobic interactions: K:F.329 Hydrogen bonds: K:N.193, K:S.247, K:G.289 Water bridges: K:G.289, K:F.329

33 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: I.76, R.114, L.117, T.118, S.119, G.313, R.316, S.355 Ligands: GOL.4 Ligand excluded by PLIP GOL.3: 5 residues within 4Å: Chain A: R.114, K.145, R.316, G.356 Chain K: E.281 Ligand excluded by PLIP GOL.4: 6 residues within 4Å: Chain A: D.79, K.115, R.316 Chain K: E.281 Ligands: GOL.2, GOL.44 Ligand excluded by PLIP GOL.5: 8 residues within 4Å: Chain A: G.272, A.273, I.278, G.280, E.281, N.282, C.283 Chain K: K.115 Ligand excluded by PLIP GOL.6: 7 residues within 4Å: Chain A: Y.336, H.368, A.369, D.370 Chain B: K.103, V.106, L.134 Ligand excluded by PLIP GOL.7: 5 residues within 4Å: Chain A: F.216, M.434, L.451, F.452, F.453 Ligand excluded by PLIP GOL.10: 6 residues within 4Å: Chain C: R.114, V.143, K.145, R.316, G.356 Chain E: E.281 Ligand excluded by PLIP GOL.11: 8 residues within 4Å: Chain C: I.76, R.114, L.117, T.118, S.119, G.313, R.316, S.355 Ligand excluded by PLIP GOL.12: 6 residues within 4Å: Chain A: Y.136, K.139, K.140 Chain C: Q.417, L.418, R.441 Ligand excluded by PLIP GOL.13: 5 residues within 4Å: Chain C: P.154, G.155, T.156, N.420, R.422 Ligand excluded by PLIP GOL.14: 10 residues within 4Å: Chain C: G.272, A.273, I.278, G.280, E.281, N.282, C.283 Chain E: N.81, K.115 Ligands: GOL.19 Ligand excluded by PLIP GOL.17: 9 residues within 4Å: Chain E: I.76, R.114, L.117, T.118, S.119, G.313, R.316, S.355 Ligands: GOL.19 Ligand excluded by PLIP GOL.18: 5 residues within 4Å: Chain C: E.281 Chain E: R.114, K.145, R.316, G.356 Ligand excluded by PLIP GOL.19: 6 residues within 4Å: Chain C: E.281 Chain E: D.79, K.115, R.316 Ligands: GOL.14, GOL.17 Ligand excluded by PLIP GOL.20: 8 residues within 4Å: Chain C: K.115 Chain E: G.272, A.273, I.278, G.280, E.281, N.282, C.283 Ligand excluded by PLIP GOL.21: 7 residues within 4Å: Chain E: Y.336, H.368, A.369, D.370 Chain F: K.103, V.106, L.134 Ligand excluded by PLIP GOL.22: 5 residues within 4Å: Chain E: F.216, M.434, L.451, F.452, F.453 Ligand excluded by PLIP GOL.25: 6 residues within 4Å: Chain G: R.114, V.143, K.145, R.316, G.356 Chain I: E.281 Ligand excluded by PLIP GOL.26: 8 residues within 4Å: Chain G: I.76, R.114, L.117, T.118, S.119, G.313, R.316, S.355 Ligand excluded by PLIP GOL.27: 6 residues within 4Å: Chain E: Y.136, K.139, K.140 Chain G: Q.417, L.418, R.441 Ligand excluded by PLIP GOL.28: 5 residues within 4Å: Chain G: P.154, G.155, T.156, N.420, R.422 Ligand excluded by PLIP GOL.29: 10 residues within 4Å: Chain G: G.272, A.273, I.278, G.280, E.281, N.282, C.283 Chain I: N.81, K.115 Ligands: GOL.34 Ligand excluded by PLIP GOL.32: 9 residues within 4Å: Chain I: I.76, R.114, L.117, T.118, S.119, G.313, R.316, S.355 Ligands: GOL.34 Ligand excluded by PLIP GOL.33: 5 residues within 4Å: Chain G: E.281 Chain I: R.114, K.145, R.316, G.356 Ligand excluded by PLIP GOL.34: 6 residues within 4Å: Chain G: E.281 Chain I: D.79, K.115, R.316 Ligands: GOL.29, GOL.32 Ligand excluded by PLIP GOL.35: 8 residues within 4Å: Chain G: K.115 Chain I: G.272, A.273, I.278, G.280, E.281, N.282, C.283 Ligand excluded by PLIP GOL.36: 7 residues within 4Å: Chain I: Y.336, H.368, A.369, D.370 Chain J: K.103, V.106, L.134 Ligand excluded by PLIP GOL.37: 5 residues within 4Å: Chain I: F.216, M.434, L.451, F.452, F.453 Ligand excluded by PLIP GOL.40: 6 residues within 4Å: Chain A: E.281 Chain K: R.114, V.143, K.145, R.316, G.356 Ligand excluded by PLIP GOL.41: 8 residues within 4Å: Chain K: I.76, R.114, L.117, T.118, S.119, G.313, R.316, S.355 Ligand excluded by PLIP GOL.42: 6 residues within 4Å: Chain I: Y.136, K.139, K.140 Chain K: Q.417, L.418, R.441 Ligand excluded by PLIP GOL.43: 5 residues within 4Å: Chain K: P.154, G.155, T.156, N.420, R.422 Ligand excluded by PLIP GOL.44: 10 residues within 4Å: Chain A: N.81, K.115 Chain K: G.272, A.273, I.278, G.280, E.281, N.282, C.283 Ligands: GOL.4 Ligand excluded by PLIP

6 x B12: COBALAMIN(Non-covalent)

B12.8: 34 residues within 4Å: Chain A: 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 B: Y.133, R.141, L.169, R.206, V.207, K.208, G.227, E.228, R.229, Y.241, E.253, A.254, R.256, C.258, S.260, N.261 Ligands: 5AD.1 35 PLIP interactions: 12 interactions with chain A, 22 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: A:F.258, A:F.329, A:F.329, A:F.329, A:L.402, B:L.169, B:Y.241, B:E.253, B:R.256 Hydrogen bonds: A:P.194, A:L.225, A:Q.246, A:E.257, A:S.295, A:S.295, B:R.141, B:V.207, B:K.208, B:E.228, B:R.229, B:Y.241, B:E.253, B:C.258, B:N.261 Water bridges: A:N.193, B:R.206, B:R.206, B:R.206, B:R.206, B:K.208, B:E.228, B:S.239, B:C.258 Salt bridges: B:R.206 Metal complexes: B12.8 B12.15: 32 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.133, R.141, L.169, R.206, V.207, K.208, G.227, E.228, R.229, Y.241, E.253, R.256, C.258, S.260 Ligands: 5AD.9 34 PLIP interactions: 19 interactions with chain D, 14 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: D:L.169, D:Y.241, D:E.253, D:R.256, C:F.258, C:F.329, C:F.329, C:I.330, C:L.402 Hydrogen bonds: D:V.207, D:E.228, D:R.229, D:Y.241, D:Y.241, D:C.258, D:N.261, C:P.194, C:L.225, C:Q.246, C:S.247, C:E.257, C:S.295, C:S.295 Water bridges: D:R.141, D:R.206, D:R.206, D:R.206, D:R.206, D:K.208, D:C.258, C:N.193, C:Y.334 Salt bridges: D:R.206 Metal complexes: B12.15 B12.23: 34 residues within 4Å: Chain E: 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 F: Y.133, R.141, L.169, R.206, V.207, K.208, G.227, E.228, R.229, Y.241, E.253, A.254, R.256, C.258, S.260, N.261 Ligands: 5AD.16 35 PLIP interactions: 22 interactions with chain F, 12 interactions with chain E, 1 Ligand-Ligand interactions Hydrophobic interactions: F:L.169, F:Y.241, F:E.253, F:R.256, E:F.258, E:F.329, E:F.329, E:F.329, E:L.402 Hydrogen bonds: F:R.141, F:V.207, F:K.208, F:E.228, F:R.229, F:Y.241, F:E.253, F:C.258, F:N.261, E:P.194, E:L.225, E:Q.246, E:E.257, E:S.295, E:S.295 Water bridges: F:R.206, F:R.206, F:R.206, F:R.206, F:K.208, F:E.228, F:S.239, F:C.258, E:N.193 Salt bridges: F:R.206 Metal complexes: B12.23 B12.30: 32 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.133, R.141, L.169, R.206, V.207, K.208, G.227, E.228, R.229, Y.241, E.253, R.256, C.258, S.260 Ligands: 5AD.24 34 PLIP interactions: 19 interactions with chain H, 14 interactions with chain G, 1 Ligand-Ligand interactions Hydrophobic interactions: H:L.169, H:Y.241, H:E.253, H:R.256, G:F.258, G:F.329, G:F.329, G:I.330, G:L.402 Hydrogen bonds: H:V.207, H:E.228, H:R.229, H:Y.241, H:Y.241, H:C.258, H:N.261, G:P.194, G:L.225, G:Q.246, G:S.247, G:E.257, G:S.295, G:S.295 Water bridges: H:R.141, H:R.206, H:R.206, H:R.206, H:R.206, H:K.208, H:C.258, G:N.193, G:Y.334 Salt bridges: H:R.206 Metal complexes: B12.30 B12.38: 34 residues within 4Å: Chain I: 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 J: Y.133, R.141, L.169, R.206, V.207, K.208, G.227, E.228, R.229, Y.241, E.253, A.254, R.256, C.258, S.260, N.261 Ligands: 5AD.31 35 PLIP interactions: 22 interactions with chain J, 12 interactions with chain I, 1 Ligand-Ligand interactions Hydrophobic interactions: J:L.169, J:Y.241, J:E.253, J:R.256, I:F.258, I:F.329, I:F.329, I:F.329, I:L.402 Hydrogen bonds: J:R.141, J:V.207, J:K.208, J:E.228, J:R.229, J:Y.241, J:E.253, J:C.258, J:N.261, I:P.194, I:L.225, I:Q.246, I:E.257, I:S.295, I:S.295 Water bridges: J:R.206, J:R.206, J:R.206, J:R.206, J:K.208, J:E.228, J:S.239, J:C.258, I:N.193 Salt bridges: J:R.206 Metal complexes: B12.38 B12.45: 32 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.133, R.141, L.169, R.206, V.207, K.208, G.227, E.228, R.229, Y.241, E.253, R.256, C.258, S.260 Ligands: 5AD.39 34 PLIP interactions: 14 interactions with chain K, 19 interactions with chain L, 1 Ligand-Ligand interactions Hydrophobic interactions: K:F.258, K:F.329, K:F.329, K:I.330, K:L.402, L:L.169, L:Y.241, L:E.253, L:R.256 Hydrogen bonds: K:P.194, K:L.225, K:Q.246, K:S.247, K:E.257, K:S.295, K:S.295, L:V.207, L:E.228, L:R.229, L:Y.241, L:Y.241, L:C.258, L:N.261 Water bridges: K:N.193, K:Y.334, L:R.141, L:R.206, L:R.206, L:R.206, L:R.206, L:K.208, L:C.258 Salt bridges: L:R.206 Metal complexes: B12.45

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shibata, N. et al., Direct Participation of a Peripheral Side Chain of a Corrin Ring in Coenzyme B12Catalysis. Angew. Chem. Int. Ed. Engl. (2018)

Release Date

2018-09-19

Peptides

Ethanolamine ammonia-lyase heavy chain: ACEGIK
Ethanolamine ammonia-lyase light chain: 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 heavy chain

Ethanolamine ammonia-lyase light chain

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