- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.35 Å
- Oligo State
- hetero-12-12-mer
- Ligands
- 40 x 3N8: 4-fluorobenzene-1,2-diol(Non-covalent)
- 4 x SO4: SULFATE ION(Non-functional Binders)
SO4.2: 4 residues within 4Å:- Chain A: N.37, R.38, T.105, H.107
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:N.37, A:T.105
- Water bridges: A:N.37, A:R.38
- Salt bridges: A:R.38, A:H.107
SO4.25: 4 residues within 4Å:- Chain G: N.37, R.38, T.105, H.107
6 PLIP interactions:6 interactions with chain G- Hydrogen bonds: G:N.37, G:T.105
- Water bridges: G:N.37, G:R.38
- Salt bridges: G:R.38, G:H.107
SO4.48: 4 residues within 4Å:- Chain M: N.37, R.38, T.105, H.107
5 PLIP interactions:5 interactions with chain M- Hydrogen bonds: M:N.37
- Water bridges: M:N.37, M:R.38
- Salt bridges: M:R.38, M:H.107
SO4.71: 4 residues within 4Å:- Chain S: N.37, R.38, T.105, H.107
5 PLIP interactions:5 interactions with chain S- Hydrogen bonds: S:N.37
- Water bridges: S:N.37, S:R.38
- Salt bridges: S:R.38, S:H.107
- 12 x FE: FE (III) ION(Non-covalent)
FE.3: 4 residues within 4Å:- Chain B: Y.108, H.160, H.162
- Ligands: 3N8.7
3 PLIP interactions:3 interactions with chain B- Metal complexes: B:Y.108, B:H.160, B:H.162
FE.15: 4 residues within 4Å:- Chain E: Y.108, H.160, H.162
- Ligands: 3N8.16
3 PLIP interactions:3 interactions with chain E- Metal complexes: E:Y.108, E:H.160, E:H.162
FE.18: 5 residues within 4Å:- Chain F: Y.108, Y.147, H.160, H.162
- Ligands: 3N8.20
4 PLIP interactions:4 interactions with chain F- Metal complexes: F:Y.108, F:Y.147, F:H.160, F:H.162
FE.26: 4 residues within 4Å:- Chain H: Y.108, H.160, H.162
- Ligands: 3N8.30
3 PLIP interactions:3 interactions with chain H- Metal complexes: H:Y.108, H:H.160, H:H.162
FE.38: 4 residues within 4Å:- Chain K: Y.108, H.160, H.162
- Ligands: 3N8.39
3 PLIP interactions:3 interactions with chain K- Metal complexes: K:Y.108, K:H.160, K:H.162
FE.41: 5 residues within 4Å:- Chain L: Y.108, Y.147, H.160, H.162
- Ligands: 3N8.43
4 PLIP interactions:4 interactions with chain L- Metal complexes: L:Y.108, L:Y.147, L:H.160, L:H.162
FE.49: 4 residues within 4Å:- Chain N: Y.108, H.160, H.162
- Ligands: 3N8.53
3 PLIP interactions:3 interactions with chain N- Metal complexes: N:Y.108, N:H.160, N:H.162
FE.61: 4 residues within 4Å:- Chain Q: Y.108, H.160, H.162
- Ligands: 3N8.62
3 PLIP interactions:3 interactions with chain Q- Metal complexes: Q:Y.108, Q:H.160, Q:H.162
FE.64: 5 residues within 4Å:- Chain R: Y.108, Y.147, H.160, H.162
- Ligands: 3N8.66
4 PLIP interactions:4 interactions with chain R- Metal complexes: R:Y.108, R:Y.147, R:H.160, R:H.162
FE.72: 4 residues within 4Å:- Chain T: Y.108, H.160, H.162
- Ligands: 3N8.76
3 PLIP interactions:3 interactions with chain T- Metal complexes: T:Y.108, T:H.160, T:H.162
FE.84: 4 residues within 4Å:- Chain W: Y.108, H.160, H.162
- Ligands: 3N8.85
3 PLIP interactions:3 interactions with chain W- Metal complexes: W:Y.108, W:H.160, W:H.162
FE.87: 5 residues within 4Å:- Chain X: Y.108, Y.147, H.160, H.162
- Ligands: 3N8.89
4 PLIP interactions:4 interactions with chain X- Metal complexes: X:Y.108, X:Y.147, X:H.160, X:H.162
- 16 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)
BME.5: 5 residues within 4Å:- Chain A: P.1, I.2, E.3
- Chain B: M.188
- Chain N: M.210
Ligand excluded by PLIPBME.12: 2 residues within 4Å:- Chain D: V.113, A.151
Ligand excluded by PLIPBME.13: 4 residues within 4Å:- Chain D: N.116, L.160
- Chain E: P.40
- Ligands: 3N8.21
Ligand excluded by PLIPBME.19: 5 residues within 4Å:- Chain D: P.1, I.2, E.3
- Chain F: M.188
- Chain L: M.210
Ligand excluded by PLIPBME.28: 5 residues within 4Å:- Chain G: P.1, I.2, E.3
- Chain H: M.188
- Chain T: M.210
Ligand excluded by PLIPBME.35: 2 residues within 4Å:- Chain J: V.113, A.151
Ligand excluded by PLIPBME.36: 4 residues within 4Å:- Chain J: N.116, L.160
- Chain K: P.40
- Ligands: 3N8.44
Ligand excluded by PLIPBME.42: 5 residues within 4Å:- Chain F: M.210
- Chain J: P.1, I.2, E.3
- Chain L: M.188
Ligand excluded by PLIPBME.51: 5 residues within 4Å:- Chain B: M.210
- Chain M: P.1, I.2, E.3
- Chain N: M.188
Ligand excluded by PLIPBME.58: 2 residues within 4Å:- Chain P: V.113, A.151
Ligand excluded by PLIPBME.59: 4 residues within 4Å:- Chain P: N.116, L.160
- Chain Q: P.40
- Ligands: 3N8.67
Ligand excluded by PLIPBME.65: 5 residues within 4Å:- Chain P: P.1, I.2, E.3
- Chain R: M.188
- Chain X: M.210
Ligand excluded by PLIPBME.74: 5 residues within 4Å:- Chain H: M.210
- Chain S: P.1, I.2, E.3
- Chain T: M.188
Ligand excluded by PLIPBME.81: 2 residues within 4Å:- Chain V: V.113, A.151
Ligand excluded by PLIPBME.82: 4 residues within 4Å:- Chain V: N.116, L.160
- Chain W: P.40
- Ligands: 3N8.90
Ligand excluded by PLIPBME.88: 5 residues within 4Å:- Chain R: M.210
- Chain V: P.1, I.2, E.3
- Chain X: M.188
Ligand excluded by PLIP- 12 x CL: CHLORIDE ION(Non-functional Binders)
CL.8: 3 residues within 4Å:- Chain B: R.107, P.118, L.119
Ligand excluded by PLIPCL.22: 3 residues within 4Å:- Chain F: R.109, H.110, L.119
Ligand excluded by PLIPCL.23: 2 residues within 4Å:- Chain F: W.149, R.150
Ligand excluded by PLIPCL.31: 3 residues within 4Å:- Chain H: R.107, P.118, L.119
Ligand excluded by PLIPCL.45: 3 residues within 4Å:- Chain L: R.109, H.110, L.119
Ligand excluded by PLIPCL.46: 2 residues within 4Å:- Chain L: W.149, R.150
Ligand excluded by PLIPCL.54: 3 residues within 4Å:- Chain N: R.107, P.118, L.119
Ligand excluded by PLIPCL.68: 3 residues within 4Å:- Chain R: R.109, H.110, L.119
Ligand excluded by PLIPCL.69: 2 residues within 4Å:- Chain R: W.149, R.150
Ligand excluded by PLIPCL.77: 3 residues within 4Å:- Chain T: R.107, P.118, L.119
Ligand excluded by PLIPCL.91: 3 residues within 4Å:- Chain X: R.109, H.110, L.119
Ligand excluded by PLIPCL.92: 2 residues within 4Å:- Chain X: W.149, R.150
Ligand excluded by PLIP- 8 x MUC: [(2S)-5-oxo-2,5-dihydrofuran-2-yl]acetic acid(Non-covalent)
MUC.10: 9 residues within 4Å:- Chain C: E.168, T.169, I.171, A.172, K.173, R.184, F.185, D.186, R.188
5 PLIP interactions:5 interactions with chain C- Hydrophobic interactions: C:F.185
- Hydrogen bonds: C:D.186
- Salt bridges: C:K.173, C:K.173, C:R.188
MUC.14: 8 residues within 4Å:- Chain D: E.168, T.169, I.171, A.172, R.184, F.185, D.186, R.188
4 PLIP interactions:4 interactions with chain D- Hydrophobic interactions: D:F.185
- Hydrogen bonds: D:D.186
- Salt bridges: D:K.173, D:R.188
MUC.33: 9 residues within 4Å:- Chain I: E.168, T.169, I.171, A.172, K.173, R.184, F.185, D.186, R.188
5 PLIP interactions:5 interactions with chain I- Hydrophobic interactions: I:F.185
- Hydrogen bonds: I:D.186
- Salt bridges: I:K.173, I:K.173, I:R.188
MUC.37: 8 residues within 4Å:- Chain J: E.168, T.169, I.171, A.172, R.184, F.185, D.186, R.188
4 PLIP interactions:4 interactions with chain J- Hydrophobic interactions: J:F.185
- Hydrogen bonds: J:D.186
- Salt bridges: J:K.173, J:R.188
MUC.56: 9 residues within 4Å:- Chain O: E.168, T.169, I.171, A.172, K.173, R.184, F.185, D.186, R.188
5 PLIP interactions:5 interactions with chain O- Hydrophobic interactions: O:F.185
- Hydrogen bonds: O:D.186
- Salt bridges: O:K.173, O:K.173, O:R.188
MUC.60: 8 residues within 4Å:- Chain P: E.168, T.169, I.171, A.172, R.184, F.185, D.186, R.188
4 PLIP interactions:4 interactions with chain P- Hydrophobic interactions: P:F.185
- Hydrogen bonds: P:D.186
- Salt bridges: P:K.173, P:R.188
MUC.79: 9 residues within 4Å:- Chain U: E.168, T.169, I.171, A.172, K.173, R.184, F.185, D.186, R.188
5 PLIP interactions:5 interactions with chain U- Hydrophobic interactions: U:F.185
- Hydrogen bonds: U:D.186
- Salt bridges: U:K.173, U:K.173, U:R.188
MUC.83: 8 residues within 4Å:- Chain V: E.168, T.169, I.171, A.172, R.184, F.185, D.186, R.188
4 PLIP interactions:4 interactions with chain V- Hydrophobic interactions: V:F.185
- Hydrogen bonds: V:D.186
- Salt bridges: V:K.173, V:R.188
- 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: ACDGIJMOPSUV
Protocatechuate 3,4-dioxygenase beta chain: BEFHKLNQRTWX - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AC
ED
CG
AI
EJ
CM
AO
EP
CS
AU
EV
CB
FE
DF
BH
FK
DL
BN
FQ
DR
BT
FW
DX
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.35 Å
- Oligo State
- hetero-12-12-mer
- Ligands
- 40 x 3N8: 4-fluorobenzene-1,2-diol(Non-covalent)
- 4 x SO4: SULFATE ION(Non-functional Binders)
- 12 x FE: FE (III) ION(Non-covalent)
- 16 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)
- 12 x CL: CHLORIDE ION(Non-functional Binders)
- 8 x MUC: [(2S)-5-oxo-2,5-dihydrofuran-2-yl]acetic acid(Non-covalent)
- 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: ACDGIJMOPSUV
Protocatechuate 3,4-dioxygenase beta chain: BEFHKLNQRTWX - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AC
ED
CG
AI
EJ
CM
AO
EP
CS
AU
EV
CB
FE
DF
BH
FK
DL
BN
FQ
DR
BT
FW
DX
B