- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.79 Å
- Oligo State
- homo-pentamer
- Ligands
- 7 x NA: SODIUM ION(Non-functional Binders)
- 5 x FEC: 1,3,5,8-TETRAMETHYL-PORPHINE-2,4,6,7-TETRAPROPIONIC ACID FERROUS COMPLEX(Non-covalent)(Covalent)
FEC.2: 23 residues within 4Å:- Chain A: S.111, Y.113, L.114, Y.147, M.149, K.151, W.159, I.171, H.174, G.175, G.178, R.179, Y.181, Q.187, I.189, W.200, V.202, L.204, I.215, V.216, M.219, S.225, F.231
15 PLIP interactions:15 interactions with chain A,- Hydrophobic interactions: A:L.114, A:Y.147, A:I.171, A:L.204
- Hydrogen bonds: A:W.159, A:Q.187, A:W.200, A:S.225
- Water bridges: A:Y.113, A:H.174, A:H.174
- Salt bridges: A:K.151, A:H.174, A:R.179
- Metal complexes: A:H.174
FEC.5: 22 residues within 4Å:- Chain B: L.110, S.111, R.133, Y.147, M.149, K.151, W.159, I.171, H.174, G.175, G.178, R.179, Q.187, I.189, W.200, V.202, L.204, I.215, V.216, M.219, S.225, F.231
16 PLIP interactions:16 interactions with chain B,- Hydrophobic interactions: B:Q.187, B:W.200, B:W.200, B:V.202, B:L.204, B:I.215
- Hydrogen bonds: B:S.111, B:Y.147, B:W.159, B:S.225, B:S.225
- Water bridges: B:W.200, B:R.220
- Salt bridges: B:R.133, B:R.133, B:K.151
FEC.8: 24 residues within 4Å:- Chain C: S.111, Y.113, R.133, Y.147, M.149, K.151, W.159, I.171, H.174, G.175, G.178, R.179, Y.181, A.182, Q.187, I.189, W.200, V.202, L.204, I.215, V.216, M.219, S.225, F.231
17 PLIP interactions:17 interactions with chain C,- Hydrophobic interactions: C:Q.187, C:I.189, C:W.200, C:V.202, C:V.202, C:I.215
- Hydrogen bonds: C:Y.147, C:Y.147, C:W.159
- Water bridges: C:Y.113, C:W.200
- Salt bridges: C:R.133, C:R.133, C:K.151, C:H.174
- pi-Stacking: C:H.174, C:H.174
FEC.14: 24 residues within 4Å:- Chain D: S.111, Y.113, L.114, R.133, Y.147, M.149, K.151, W.159, I.171, H.174, G.175, G.178, R.179, Y.181, Q.187, I.189, W.200, V.202, L.204, I.215, V.216, M.219, S.225, F.231
22 PLIP interactions:22 interactions with chain D,- Hydrophobic interactions: D:Y.147, D:I.171, D:Q.187, D:W.200, D:L.204, D:F.231
- Hydrogen bonds: D:W.159, D:Q.187, D:W.200, D:S.225
- Water bridges: D:E.109, D:E.109, D:Y.113, D:H.174, D:H.174, D:R.179
- Salt bridges: D:R.133, D:K.151, D:H.174, D:R.179, D:R.179
- Metal complexes: D:H.174
FEC.21: 25 residues within 4Å:- Chain E: V.5, L.110, S.111, Y.113, R.133, Y.147, M.149, K.151, W.159, I.171, H.174, G.175, G.178, R.179, Y.181, Q.187, I.189, W.200, V.202, L.204, I.215, V.216, M.219, S.225, F.231
19 PLIP interactions:19 interactions with chain E,- Hydrophobic interactions: E:I.171, E:I.171, E:Q.187, E:W.200, E:V.202, E:L.204, E:I.215
- Hydrogen bonds: E:Y.147, E:W.159, E:S.225, E:S.225
- Water bridges: E:Y.113, E:Y.113, E:R.220
- Salt bridges: E:R.133, E:K.151, E:R.179, E:R.179
- Metal complexes: E:H.174
- 10 x POL: N-PROPANOL(Non-covalent)
POL.6: 4 residues within 4Å:- Chain B: K.67, Y.102, S.233, F.235
1 PLIP interactions:1 interactions with chain B- Hydrophobic interactions: B:Y.102
POL.7: 5 residues within 4Å:- Chain A: G.232, S.233
- Chain B: D.197, Y.198, E.230
1 PLIP interactions:1 interactions with chain A- Water bridges: A:S.233
POL.9: 3 residues within 4Å:- Chain C: Y.102, S.233, F.235
1 PLIP interactions:1 interactions with chain C- Water bridges: C:T.101
POL.10: 6 residues within 4Å:- Chain C: S.150, D.197, Y.198
- Chain D: F.231, G.232, S.233
2 PLIP interactions:1 interactions with chain D, 1 interactions with chain C- Water bridges: D:S.233
- Hydrophobic interactions: C:Y.198
POL.11: 4 residues within 4Å:- Chain C: L.8, Q.126, N.127, V.130
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:N.127
POL.15: 3 residues within 4Å:- Chain D: P.100, T.101
- Ligands: POL.17
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:T.101
POL.16: 2 residues within 4Å:- Chain D: D.197, Y.198
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:D.197
POL.17: 6 residues within 4Å:- Chain D: K.67, T.101, Y.102, S.233, F.235
- Ligands: POL.15
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:K.67
POL.22: 4 residues within 4Å:- Chain E: K.67, Y.102, S.233, F.235
1 PLIP interactions:1 interactions with chain E- Hydrophobic interactions: E:Y.102
POL.23: 3 residues within 4Å:- Chain E: S.150, D.197, Y.198
1 PLIP interactions:1 interactions with chain E- Hydrophobic interactions: E:Y.198
- 1 x CL: CHLORIDE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Milazzo, L. et al., Redox Cofactor Rotates during Its Stepwise Decarboxylation: Molecular Mechanism of Conversion of Coproheme to Hemeb. Acs Catalysis (2019)
- Release Date
- 2019-07-10
- Peptides
- Putative heme-dependent peroxidase lmo2113: ABCDE
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
E
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.79 Å
- Oligo State
- homo-pentamer
- Ligands
- 7 x NA: SODIUM ION(Non-functional Binders)
- 5 x FEC: 1,3,5,8-TETRAMETHYL-PORPHINE-2,4,6,7-TETRAPROPIONIC ACID FERROUS COMPLEX(Non-covalent)(Covalent)
- 10 x POL: N-PROPANOL(Non-covalent)
- 1 x CL: CHLORIDE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Milazzo, L. et al., Redox Cofactor Rotates during Its Stepwise Decarboxylation: Molecular Mechanism of Conversion of Coproheme to Hemeb. Acs Catalysis (2019)
- Release Date
- 2019-07-10
- Peptides
- Putative heme-dependent peroxidase lmo2113: ABCDE
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
E