- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.58 Å
- Oligo State
- hetero-12-12-mer
- Ligands
- 56 x 3N8: 4-fluorobenzene-1,2-diol(Non-covalent)
- 16 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)
BME.2: 7 residues within 4Å:- Chain A: E.69, F.92, R.94
- Chain E: P.49, F.51, S.166, K.173
Ligand excluded by PLIPBME.16: 6 residues within 4Å:- Chain E: Y.115, L.116, A.117
- Chain K: R.77, M.216, D.217
Ligand excluded by PLIPBME.22: 3 residues within 4Å:- Chain A: I.2
- Chain F: M.188
- Chain R: M.210
Ligand excluded by PLIPBME.23: 6 residues within 4Å:- Chain F: Y.115, L.116, A.117
- Chain R: R.77, M.216, D.217
Ligand excluded by PLIPBME.26: 7 residues within 4Å:- Chain G: E.69, F.92, R.94
- Chain K: P.49, F.51, S.166, K.173
Ligand excluded by PLIPBME.40: 6 residues within 4Å:- Chain E: R.77, M.216, D.217
- Chain K: Y.115, L.116, A.117
Ligand excluded by PLIPBME.46: 3 residues within 4Å:- Chain G: I.2
- Chain L: M.188
- Chain X: M.210
Ligand excluded by PLIPBME.47: 6 residues within 4Å:- Chain L: Y.115, L.116, A.117
- Chain X: R.77, M.216, D.217
Ligand excluded by PLIPBME.50: 7 residues within 4Å:- Chain M: E.69, F.92, R.94
- Chain Q: P.49, F.51, S.166, K.173
Ligand excluded by PLIPBME.64: 6 residues within 4Å:- Chain Q: Y.115, L.116, A.117
- Chain W: R.77, M.216, D.217
Ligand excluded by PLIPBME.70: 3 residues within 4Å:- Chain F: M.210
- Chain M: I.2
- Chain R: M.188
Ligand excluded by PLIPBME.71: 6 residues within 4Å:- Chain F: R.77, M.216, D.217
- Chain R: Y.115, L.116, A.117
Ligand excluded by PLIPBME.74: 7 residues within 4Å:- Chain S: E.69, F.92, R.94
- Chain W: P.49, F.51, S.166, K.173
Ligand excluded by PLIPBME.88: 6 residues within 4Å:- Chain Q: R.77, M.216, D.217
- Chain W: Y.115, L.116, A.117
Ligand excluded by PLIPBME.94: 3 residues within 4Å:- Chain L: M.210
- Chain S: I.2
- Chain X: M.188
Ligand excluded by PLIPBME.95: 6 residues within 4Å:- Chain L: R.77, M.216, D.217
- Chain X: Y.115, L.116, A.117
Ligand excluded by PLIP- 12 x FE: FE (III) ION(Non-covalent)
FE.5: 4 residues within 4Å:- Chain D: Y.108, Y.147, H.160, H.162
5 PLIP interactions:4 interactions with chain D, 1 Ligand-Water interactions- Metal complexes: D:Y.108, D:Y.147, D:H.160, D:H.162, H2O.22
FE.11: 5 residues within 4Å:- Chain E: Y.108, Y.147, H.160, H.162
- Ligands: 3NJ.17
5 PLIP interactions:4 interactions with chain E, 1 Ligand-Water interactions- Metal complexes: E:Y.108, E:Y.147, E:H.160, E:H.162, H2O.30
FE.24: 4 residues within 4Å:- Chain F: Y.108, Y.147, H.160, H.162
5 PLIP interactions:4 interactions with chain F, 1 Ligand-Water interactions- Metal complexes: F:Y.108, F:Y.147, F:H.160, F:H.162, H2O.36
FE.29: 4 residues within 4Å:- Chain J: Y.108, Y.147, H.160, H.162
5 PLIP interactions:4 interactions with chain J, 1 Ligand-Water interactions- Metal complexes: J:Y.108, J:Y.147, J:H.160, J:H.162, H2O.59
FE.35: 5 residues within 4Å:- Chain K: Y.108, Y.147, H.160, H.162
- Ligands: 3NJ.41
5 PLIP interactions:4 interactions with chain K, 1 Ligand-Water interactions- Metal complexes: K:Y.108, K:Y.147, K:H.160, K:H.162, H2O.66
FE.48: 4 residues within 4Å:- Chain L: Y.108, Y.147, H.160, H.162
5 PLIP interactions:4 interactions with chain L, 1 Ligand-Water interactions- Metal complexes: L:Y.108, L:Y.147, L:H.160, L:H.162, H2O.73
FE.53: 4 residues within 4Å:- Chain P: Y.108, Y.147, H.160, H.162
5 PLIP interactions:4 interactions with chain P, 1 Ligand-Water interactions- Metal complexes: P:Y.108, P:Y.147, P:H.160, P:H.162, H2O.95
FE.59: 5 residues within 4Å:- Chain Q: Y.108, Y.147, H.160, H.162
- Ligands: 3NJ.65
5 PLIP interactions:4 interactions with chain Q, 1 Ligand-Water interactions- Metal complexes: Q:Y.108, Q:Y.147, Q:H.160, Q:H.162, H2O.102
FE.72: 4 residues within 4Å:- Chain R: Y.108, Y.147, H.160, H.162
5 PLIP interactions:4 interactions with chain R, 1 Ligand-Water interactions- Metal complexes: R:Y.108, R:Y.147, R:H.160, R:H.162, H2O.109
FE.77: 4 residues within 4Å:- Chain V: Y.108, Y.147, H.160, H.162
5 PLIP interactions:4 interactions with chain V, 1 Ligand-Water interactions- Metal complexes: V:Y.108, V:Y.147, V:H.160, V:H.162, H2O.132
FE.83: 5 residues within 4Å:- Chain W: Y.108, Y.147, H.160, H.162
- Ligands: 3NJ.89
5 PLIP interactions:4 interactions with chain W, 1 Ligand-Water interactions- Metal complexes: W:Y.108, W:Y.147, W:H.160, W:H.162, H2O.139
FE.96: 4 residues within 4Å:- Chain X: Y.108, Y.147, H.160, H.162
5 PLIP interactions:4 interactions with chain X, 1 Ligand-Water interactions- Metal complexes: X:Y.108, X:Y.147, X:H.160, X:H.162, H2O.146
- 4 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)
TRS.14: 6 residues within 4Å:- Chain D: R.33
- Chain E: R.33
- Chain F: R.33
- Ligands: 3N8.9, 3N8.12, 3N8.19
6 PLIP interactions:2 interactions with chain D, 2 interactions with chain F, 2 interactions with chain E- Hydrogen bonds: D:R.33, D:R.33, F:R.33, F:R.33, E:R.33, E:R.33
TRS.38: 6 residues within 4Å:- Chain J: R.33
- Chain K: R.33
- Chain L: R.33
- Ligands: 3N8.33, 3N8.36, 3N8.43
6 PLIP interactions:2 interactions with chain L, 2 interactions with chain K, 2 interactions with chain J- Hydrogen bonds: L:R.33, L:R.33, K:R.33, K:R.33, J:R.33, J:R.33
TRS.62: 6 residues within 4Å:- Chain P: R.33
- Chain Q: R.33
- Chain R: R.33
- Ligands: 3N8.57, 3N8.60, 3N8.67
6 PLIP interactions:2 interactions with chain P, 2 interactions with chain Q, 2 interactions with chain R- Hydrogen bonds: P:R.33, P:R.33, Q:R.33, Q:R.33, R:R.33, R:R.33
TRS.86: 6 residues within 4Å:- Chain V: R.33
- Chain W: R.33
- Chain X: R.33
- Ligands: 3N8.81, 3N8.84, 3N8.91
6 PLIP interactions:2 interactions with chain W, 2 interactions with chain V, 2 interactions with chain X- Hydrogen bonds: W:R.33, W:R.33, V:R.33, V:R.33, X:R.33, X:R.33
- 4 x 3NJ: 4-fluorooxepine-2,7-dione(Non-covalent)
3NJ.17: 13 residues within 4Å:- Chain A: T.12, G.14, P.15
- Chain E: Y.24, Y.108, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191
- Ligands: FE.11
11 PLIP interactions:11 interactions with chain E- Hydrophobic interactions: E:Y.147, E:W.149, E:R.157, E:I.191
- Hydrogen bonds: E:Q.177
- Salt bridges: E:R.157, E:R.157, E:H.160, E:H.160, E:H.162, E:H.162
3NJ.41: 13 residues within 4Å:- Chain G: T.12, G.14, P.15
- Chain K: Y.24, Y.108, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191
- Ligands: FE.35
11 PLIP interactions:11 interactions with chain K- Hydrophobic interactions: K:Y.147, K:W.149, K:R.157, K:I.191
- Hydrogen bonds: K:Q.177
- Salt bridges: K:R.157, K:R.157, K:H.160, K:H.160, K:H.162, K:H.162
3NJ.65: 13 residues within 4Å:- Chain M: T.12, G.14, P.15
- Chain Q: Y.24, Y.108, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191
- Ligands: FE.59
11 PLIP interactions:11 interactions with chain Q- Hydrophobic interactions: Q:Y.147, Q:W.149, Q:R.157, Q:I.191
- Hydrogen bonds: Q:Q.177
- Salt bridges: Q:R.157, Q:R.157, Q:H.160, Q:H.160, Q:H.162, Q:H.162
3NJ.89: 13 residues within 4Å:- Chain S: T.12, G.14, P.15
- Chain W: Y.24, Y.108, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191
- Ligands: FE.83
11 PLIP interactions:11 interactions with chain W- Hydrophobic interactions: W:Y.147, W:W.149, W:R.157, W:I.191
- Hydrogen bonds: W:Q.177
- Salt bridges: W:R.157, W:R.157, W:H.160, W:H.160, W:H.162, W:H.162
- 4 x CL: CHLORIDE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Knoot, C.J. et al., Crystal structures of alkylperoxo and anhydride intermediates in an intradiol ring-cleaving dioxygenase. Proc.Natl.Acad.Sci.USA (2015)
- Release Date
- 2014-12-31
- Peptides
- Protocatechuate 3,4-dioxygenase alpha chain: ABCGHIMNOSTU
Protocatechuate 3,4-dioxygenase beta chain: DEFJKLPQRVWX - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
EC
CG
AH
EI
CM
AN
EO
CS
AT
EU
CD
DE
BF
FJ
DK
BL
FP
DQ
BR
FV
DW
BX
F
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.58 Å
- Oligo State
- hetero-12-12-mer
- Ligands
- 56 x 3N8: 4-fluorobenzene-1,2-diol(Non-covalent)
- 16 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)
- 12 x FE: FE (III) ION(Non-covalent)
- 4 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)
- 4 x 3NJ: 4-fluorooxepine-2,7-dione(Non-covalent)
- 4 x CL: CHLORIDE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Knoot, C.J. et al., Crystal structures of alkylperoxo and anhydride intermediates in an intradiol ring-cleaving dioxygenase. Proc.Natl.Acad.Sci.USA (2015)
- Release Date
- 2014-12-31
- Peptides
- Protocatechuate 3,4-dioxygenase alpha chain: ABCGHIMNOSTU
Protocatechuate 3,4-dioxygenase beta chain: DEFJKLPQRVWX - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
EC
CG
AH
EI
CM
AN
EO
CS
AT
EU
CD
DE
BF
FJ
DK
BL
FP
DQ
BR
FV
DW
BX
F