- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.10 Å
- Oligo State
- hetero-6-6-mer
- Ligands
- 6 x ETA: ETHANOLAMINE(Non-covalent)
- 15 x GOL: GLYCEROL(Non-functional Binders)
GOL.2: 9 residues within 4Å:- Chain A: G.272, A.273, I.278, G.280, E.281, N.282, C.283
- Chain G: N.81, K.115
3 PLIP interactions:2 interactions with chain G, 1 interactions with chain A- Hydrogen bonds: G:N.81, G:K.115
- Water bridges: A:A.273
GOL.3: 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
6 PLIP interactions:3 interactions with chain A, 3 interactions with chain G- Hydrogen bonds: A:K.115, G:G.272, G:I.278, G:E.281
- Water bridges: A:N.81, A:N.81
GOL.4: 4 residues within 4Å:- Chain A: R.114, K.145, R.316, G.356
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:K.145, A:K.145, A:G.356
- Water bridges: A:R.114, A:D.319
GOL.8: 4 residues within 4Å:- Chain C: R.114, K.145, R.316, G.356
6 PLIP interactions:6 interactions with chain C- Hydrogen bonds: C:K.145, C:R.316
- Water bridges: C:R.114, C:I.144, C:K.145, C:R.316
GOL.9: 3 residues within 4Å:- Chain C: R.60, N.61, E.82
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:N.61, C:N.61
- Water bridges: C:E.82, C:Y.85
GOL.13: 9 residues within 4Å:- Chain E: G.272, A.273, I.278, G.280, E.281, N.282, C.283
- Chain K: N.81, K.115
3 PLIP interactions:1 interactions with chain E, 2 interactions with chain K- Water bridges: E:A.273
- Hydrogen bonds: K:N.81, K:K.115
GOL.14: 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
6 PLIP interactions:3 interactions with chain K, 3 interactions with chain E- Hydrogen bonds: K:G.272, K:I.278, K:E.281, E:K.115
- Water bridges: E:N.81, E:N.81
GOL.15: 4 residues within 4Å:- Chain E: R.114, K.145, R.316, G.356
5 PLIP interactions:5 interactions with chain E- Hydrogen bonds: E:K.145, E:K.145, E:G.356
- Water bridges: E:R.114, E:D.319
GOL.19: 4 residues within 4Å:- Chain G: R.114, K.145, R.316, G.356
6 PLIP interactions:6 interactions with chain G- Hydrogen bonds: G:K.145, G:R.316
- Water bridges: G:R.114, G:I.144, G:K.145, G:R.316
GOL.20: 3 residues within 4Å:- Chain G: R.60, N.61, E.82
4 PLIP interactions:4 interactions with chain G- Hydrogen bonds: G:N.61, G:N.61
- Water bridges: G:E.82, G:Y.85
GOL.24: 9 residues within 4Å:- Chain C: N.81, K.115
- Chain I: G.272, A.273, I.278, G.280, E.281, N.282, C.283
3 PLIP interactions:2 interactions with chain C, 1 interactions with chain I- Hydrogen bonds: C:N.81, C:K.115
- Water bridges: I:A.273
GOL.25: 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
6 PLIP interactions:3 interactions with chain C, 3 interactions with chain I- Hydrogen bonds: C:G.272, C:I.278, C:E.281, I:K.115
- Water bridges: I:N.81, I:N.81
GOL.26: 4 residues within 4Å:- Chain I: R.114, K.145, R.316, G.356
5 PLIP interactions:5 interactions with chain I- Hydrogen bonds: I:K.145, I:K.145, I:G.356
- Water bridges: I:R.114, I:D.319
GOL.30: 4 residues within 4Å:- Chain K: R.114, K.145, R.316, G.356
6 PLIP interactions:6 interactions with chain K- Hydrogen bonds: K:K.145, K:R.316
- Water bridges: K:R.114, K:I.144, K:K.145, K:R.316
GOL.31: 3 residues within 4Å:- Chain K: R.60, N.61, E.82
4 PLIP interactions:4 interactions with chain K- Hydrogen bonds: K:N.61, K:N.61
- Water bridges: K:E.82, K:Y.85
- 6 x B12: COBALAMIN(Non-covalent)
B12.5: 32 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.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
40 PLIP interactions:24 interactions with chain B, 15 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.258, A:F.329, A:F.329, A:F.329
- Hydrogen bonds: B:V.218, B:K.219, B:K.219, B:E.239, B:R.240, B:Y.252, B:Y.252, B:C.269, A:P.194, A:L.225, A:Q.246, A:S.247, A:E.257, A:S.295, A:S.295
- Water bridges: B:R.152, B:R.152, B:R.152, B:R.152, B:R.217, B:R.217, B:R.240, B:C.269, B:C.269, B:S.271, B:S.271, A:N.193, A:E.257, A:Y.334
- Salt bridges: B:R.217
- Metal complexes: B12.5
B12.10: 29 residues within 4Å:- Chain C: N.193, P.194, 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
- Chain D: Y.144, R.152, L.180, R.217, V.218, G.238, E.239, R.240, Y.252, E.264, R.267, C.269, S.271, N.272
36 PLIP interactions:21 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
- Hydrogen bonds: D:R.152, D:R.152, D:V.218, D:E.239, D:R.240, D:Y.252, D:C.269, D:N.272, C:P.194, C:A.226, C:Q.246, C:S.247, C:E.257, C:S.295, C:S.295
- Water bridges: D:R.217, D:R.217, D:R.240, D:C.269, D:C.269, D:S.271, D:S.271, D:S.271, C:N.193
- Salt bridges: D:R.217
- Metal complexes: B12.10
B12.16: 32 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.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
40 PLIP interactions:24 interactions with chain F, 15 interactions with chain E, 1 Ligand-Ligand interactions- Hydrophobic interactions: F:L.180, F:Y.252, F:E.264, F:R.267, E:F.258, E:F.258, E:F.329, E:F.329, E:F.329
- Hydrogen bonds: F:V.218, F:K.219, F:K.219, F:E.239, F:R.240, F:Y.252, F:Y.252, F:C.269, E:P.194, E:L.225, E:Q.246, E:S.247, E:E.257, E:S.295, E:S.295
- Water bridges: F:R.152, F:R.152, F:R.152, F:R.152, F:R.217, F:R.217, F:R.240, F:C.269, F:C.269, F:S.271, F:S.271, E:N.193, E:E.257, E:Y.334
- Salt bridges: F:R.217
- Metal complexes: B12.16
B12.21: 29 residues within 4Å:- Chain G: N.193, P.194, 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
- Chain H: Y.144, R.152, L.180, R.217, V.218, G.238, E.239, R.240, Y.252, E.264, R.267, C.269, S.271, N.272
36 PLIP interactions:14 interactions with chain G, 21 interactions with chain H, 1 Ligand-Ligand interactions- Hydrophobic interactions: G:F.258, G:F.258, G:F.329, G:F.329, G:F.329, G:I.330, H:L.180, H:Y.252, H:E.264, H:R.267
- Hydrogen bonds: G:P.194, G:A.226, G:Q.246, G:S.247, G:E.257, G:S.295, G:S.295, H:R.152, H:R.152, H:V.218, H:E.239, H:R.240, H:Y.252, H:C.269, H:N.272
- Water bridges: G:N.193, H:R.217, H:R.217, H:R.240, H:C.269, H:C.269, H:S.271, H:S.271, H:S.271
- Salt bridges: H:R.217
- Metal complexes: B12.21
B12.27: 32 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.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
40 PLIP interactions:24 interactions with chain J, 15 interactions with chain I, 1 Ligand-Ligand interactions- Hydrophobic interactions: J:L.180, J:Y.252, J:E.264, J:R.267, I:F.258, I:F.258, I:F.329, I:F.329, I:F.329
- Hydrogen bonds: J:V.218, J:K.219, J:K.219, J:E.239, J:R.240, J:Y.252, J:Y.252, J:C.269, I:P.194, I:L.225, I:Q.246, I:S.247, I:E.257, I:S.295, I:S.295
- Water bridges: J:R.152, J:R.152, J:R.152, J:R.152, J:R.217, J:R.217, J:R.240, J:C.269, J:C.269, J:S.271, J:S.271, I:N.193, I:E.257, I:Y.334
- Salt bridges: J:R.217
- Metal complexes: B12.27
B12.32: 29 residues within 4Å:- Chain K: N.193, P.194, 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
- Chain L: Y.144, R.152, L.180, R.217, V.218, G.238, E.239, R.240, Y.252, E.264, R.267, C.269, S.271, N.272
36 PLIP interactions:14 interactions with chain K, 21 interactions with chain L, 1 Ligand-Ligand interactions- Hydrophobic interactions: K:F.258, K:F.258, K:F.329, K:F.329, K:F.329, K:I.330, L:L.180, L:Y.252, L:E.264, L:R.267
- Hydrogen bonds: K:P.194, K:A.226, K:Q.246, K:S.247, K:E.257, K:S.295, K:S.295, L:R.152, L:R.152, L:V.218, L:E.239, L:R.240, L:Y.252, L:C.269, L:N.272
- Water bridges: K:N.193, L:R.217, L:R.217, L:R.240, L:C.269, L:C.269, L:S.271, L:S.271, L:S.271
- Salt bridges: L:R.217
- Metal complexes: B12.32
- 6 x NA: SODIUM ION(Non-functional Binders)
NA.7: 5 residues within 4Å:- Chain A: R.339
- Chain C: D.338, D.372, N.374, L.375
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:D.372, C:L.375
- Water bridges: C:N.374, C:N.378
NA.11: 4 residues within 4Å:- Chain C: E.179, H.410
- Chain D: R.88, T.91
3 PLIP interactions:2 interactions with chain D, 1 interactions with chain C- Hydrogen bonds: D:T.91, D:T.91
- Water bridges: C:H.410
NA.18: 5 residues within 4Å:- Chain E: R.339
- Chain G: D.338, D.372, N.374, L.375
4 PLIP interactions:4 interactions with chain G- Hydrogen bonds: G:D.372, G:L.375
- Water bridges: G:N.374, G:N.378
NA.22: 4 residues within 4Å:- Chain G: E.179, H.410
- Chain H: R.88, T.91
3 PLIP interactions:2 interactions with chain H, 1 interactions with chain G- Hydrogen bonds: H:T.91, H:T.91
- Water bridges: G:H.410
NA.29: 5 residues within 4Å:- Chain I: R.339
- Chain K: D.338, D.372, N.374, L.375
4 PLIP interactions:4 interactions with chain K- Hydrogen bonds: K:D.338, K:L.375
- Water bridges: K:N.374, K:N.378
NA.33: 4 residues within 4Å:- Chain K: E.179, H.410
- Chain L: R.88, T.91
3 PLIP interactions:2 interactions with chain K, 1 interactions with chain L- Hydrogen bonds: K:E.179, L:T.91
- Water bridges: K:H.410
- 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: ACEGIK
Ethanolamine ammonia-lyase light chain: BDFHJL - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AC
CE
AG
CI
AK
CB
BD
DF
BH
DJ
BL
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.10 Å
- Oligo State
- hetero-6-6-mer
- Ligands
- 6 x ETA: ETHANOLAMINE(Non-covalent)
- 15 x GOL: GLYCEROL(Non-functional Binders)
- 6 x B12: COBALAMIN(Non-covalent)
- 6 x NA: SODIUM ION(Non-functional Binders)
- 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: ACEGIK
Ethanolamine ammonia-lyase light chain: BDFHJL - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AC
CE
AG
CI
AK
CB
BD
DF
BH
DJ
BL
D