SMTL ID : 3abr.2 (1 other biounit)

Crystal structure of ethanolamine ammonia-lyase from Escherichia coli complexed with CN-Cbl (substrate-free form)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-2-2-mer

Ligands

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: G.272, A.273, I.278, G.280, E.281, N.282, C.283 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.282 Water bridges: A:A.273 GOL.2: 1 residues within 4Å: Chain A: K.115 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.115 GOL.3: 2 residues within 4Å: Chain A: N.148, R.277 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.148, A:N.148, A:R.277 Water bridges: A:I.218 GOL.9: 4 residues within 4Å: Chain C: I.144, K.145, K.146, T.150 2 PLIP interactions: 2 interactions with chain C Water bridges: C:I.144, C:T.150 GOL.10: 4 residues within 4Å: Chain C: V.143, K.145, R.316, G.356 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:K.145, C:K.145, C:R.316 Water bridges: C:R.114, C:I.144, C:R.316, C:R.316 GOL.11: 4 residues within 4Å: Chain C: R.60, N.61, E.82, Y.85 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.61, C:Y.85 Water bridges: C:E.82, C:Y.85

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

NA.4: 4 residues within 4Å: Chain A: L.294, S.295, Y.334 Chain B: P.148 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.294 NA.5: 3 residues within 4Å: Chain A: I.235, G.238, A.239 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.239 Water bridges: A:G.241 NA.6: 4 residues within 4Å: Chain A: D.398, I.400 Chain B: V.86, R.88 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.88 NA.8: 4 residues within 4Å: Chain B: L.107, H.110, S.111 Chain C: V.45 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:S.111 Water bridges: B:H.110, C:S.41, C:S.41 NA.12: 1 residues within 4Å: Chain C: D.69 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.68 NA.14: 5 residues within 4Å: Chain D: S.181, E.239, R.240, S.246, S.248 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.181, D:S.181, D:E.239, D:S.248 NA.15: 4 residues within 4Å: Chain C: V.195 Chain D: S.271, N.272, T.278 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.271 Water bridges: D:S.271

2 x B12: COBALAMIN(Non-covalent)

B12.7: 27 residues within 4Å: Chain A: N.193, P.194, V.195, S.247, E.257, F.258, S.295, F.329, I.330, M.401, L.402 Chain B: Y.144, R.152, L.180, R.217, V.218, K.219, G.238, E.239, R.240, Y.252, E.264, A.265, R.267, C.269, S.271, N.272 34 PLIP interactions: 21 interactions with chain B, 12 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: B:L.180, B:Y.252, B:E.264, B:R.267, A:F.258, A:F.329, A:F.329 Hydrogen bonds: B:V.218, B:K.219, B:E.239, B:R.240, B:Y.252, B:Y.252, B:N.272, A:P.194, A:V.195, A:S.247, A:E.257, A:S.295, A:S.295 Water bridges: B:R.152, B:R.152, B:R.217, B:R.217, B:R.217, B:K.219, B:S.250, B:C.269, B:C.269, A:N.193, A:N.193, A:Y.334 Salt bridges: B:R.217 Metal complexes: B12.7 B12.13: 25 residues within 4Å: Chain C: P.194, L.225, F.245, S.247, E.257, F.258, S.295, F.329, I.330, M.401, L.402 Chain D: Y.144, R.152, L.180, R.217, V.218, G.238, E.239, R.240, Y.252, E.264, A.265, R.267, C.269, S.271 40 PLIP interactions: 25 interactions with chain D, 14 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: D:L.180, D:Y.252, D:E.264, D:R.267, C:F.258, C:F.258, C:F.329, C:F.329, C:F.329, C:I.330, C:L.402 Hydrogen bonds: D:R.152, D:V.218, D:E.239, D:R.240, D:Y.252, D:Y.252, D:C.269, C:P.194, C:L.225, C:S.247, C:E.257, C:S.295 Water bridges: D:R.152, D:R.152, D:R.217, D:R.217, D:R.240, D:R.240, D:S.250, D:C.269, D:C.269, D:S.271, D:S.271, D:S.271, D:S.271, C:N.193, C:E.257 Salt bridges: D:R.217 Metal complexes: B12.13

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shibata, N. et al., Crystal structures of ethanolamine ammonia-lyase complexed with coenzyme B12 analogs and substrates. J.Biol.Chem. (2010)

Release Date

2010-06-02

Peptides

Ethanolamine ammonia-lyase heavy chain: AC
Ethanolamine ammonia-lyase light chain: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Ethanolamine ammonia-lyase heavy chain

Ethanolamine ammonia-lyase light chain

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