- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.86 Å
- Oligo State
- hetero-12-12-mer
- Ligands
- 28 x SO4: SULFATE ION(Non-functional Binders)
- 12 x GOL: GLYCEROL(Non-functional Binders)
GOL.3: 6 residues within 4Å:- Chain A: T.169, I.171, R.184, F.185, D.186, R.188
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:R.184, A:D.186, A:R.188
GOL.9: 7 residues within 4Å:- Chain C: T.169, I.171, A.172, R.184, F.185, D.186, R.188
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:T.169, C:D.186, C:R.188
- Water bridges: C:R.188
GOL.10: 8 residues within 4Å:- Chain C: R.38, L.39, A.40, K.41, N.84, L.85, N.87, N.90
5 PLIP interactions:5 interactions with chain C- Hydrogen bonds: C:L.39, C:K.41, C:N.87, C:N.90
- Water bridges: C:Y.83
GOL.26: 6 residues within 4Å:- Chain G: T.169, I.171, R.184, F.185, D.186, R.188
3 PLIP interactions:3 interactions with chain G- Hydrogen bonds: G:R.184, G:D.186, G:R.188
GOL.32: 7 residues within 4Å:- Chain I: T.169, I.171, A.172, R.184, F.185, D.186, R.188
4 PLIP interactions:4 interactions with chain I- Hydrogen bonds: I:T.169, I:D.186, I:R.188
- Water bridges: I:R.188
GOL.33: 8 residues within 4Å:- Chain I: R.38, L.39, A.40, K.41, N.84, L.85, N.87, N.90
5 PLIP interactions:5 interactions with chain I- Hydrogen bonds: I:L.39, I:K.41, I:N.87, I:N.90
- Water bridges: I:Y.83
GOL.49: 6 residues within 4Å:- Chain M: T.169, I.171, R.184, F.185, D.186, R.188
3 PLIP interactions:3 interactions with chain M- Hydrogen bonds: M:R.184, M:D.186, M:R.188
GOL.55: 7 residues within 4Å:- Chain O: T.169, I.171, A.172, R.184, F.185, D.186, R.188
5 PLIP interactions:5 interactions with chain O- Hydrogen bonds: O:T.169, O:D.186, O:R.188
- Water bridges: O:D.186, O:D.186
GOL.56: 8 residues within 4Å:- Chain O: R.38, L.39, A.40, K.41, N.84, L.85, N.87, N.90
4 PLIP interactions:4 interactions with chain O- Hydrogen bonds: O:L.39, O:K.41, O:N.87, O:N.90
GOL.72: 6 residues within 4Å:- Chain S: T.169, I.171, R.184, F.185, D.186, R.188
3 PLIP interactions:3 interactions with chain S- Hydrogen bonds: S:R.184, S:D.186, S:R.188
GOL.78: 7 residues within 4Å:- Chain U: T.169, I.171, A.172, R.184, F.185, D.186, R.188
5 PLIP interactions:5 interactions with chain U- Hydrogen bonds: U:T.169, U:D.186, U:R.188
- Water bridges: U:D.186, U:D.186
GOL.79: 8 residues within 4Å:- Chain U: R.38, L.39, A.40, K.41, N.84, L.85, N.87, N.90
4 PLIP interactions:4 interactions with chain U- Hydrogen bonds: U:L.39, U:K.41, U:N.87, U:N.90
- 24 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)
BME.6: 6 residues within 4Å:- Chain B: I.171, A.172, R.184, F.185, D.186, R.188
Ligand excluded by PLIPBME.7: 7 residues within 4Å:- Chain B: E.34, I.35, W.36, N.37, R.38, Y.83, L.85
Ligand excluded by PLIPBME.11: 2 residues within 4Å:- Chain D: R.109, P.121
Ligand excluded by PLIPBME.15: 2 residues within 4Å:- Chain D: I.28
- Chain E: R.33
Ligand excluded by PLIPBME.16: 4 residues within 4Å:- Chain E: T.21, P.22, D.23, K.193
Ligand excluded by PLIPBME.17: 5 residues within 4Å:- Chain E: G.57, A.58, H.59, D.60, N.66
Ligand excluded by PLIPBME.29: 6 residues within 4Å:- Chain H: I.171, A.172, R.184, F.185, D.186, R.188
Ligand excluded by PLIPBME.30: 7 residues within 4Å:- Chain H: E.34, I.35, W.36, N.37, R.38, Y.83, L.85
Ligand excluded by PLIPBME.34: 2 residues within 4Å:- Chain J: R.109, P.121
Ligand excluded by PLIPBME.38: 2 residues within 4Å:- Chain J: I.28
- Chain K: R.33
Ligand excluded by PLIPBME.39: 4 residues within 4Å:- Chain K: T.21, P.22, D.23, K.193
Ligand excluded by PLIPBME.40: 5 residues within 4Å:- Chain K: G.57, A.58, H.59, D.60, N.66
Ligand excluded by PLIPBME.52: 6 residues within 4Å:- Chain N: I.171, A.172, R.184, F.185, D.186, R.188
Ligand excluded by PLIPBME.53: 7 residues within 4Å:- Chain N: E.34, I.35, W.36, N.37, R.38, Y.83, L.85
Ligand excluded by PLIPBME.57: 2 residues within 4Å:- Chain P: R.109, P.121
Ligand excluded by PLIPBME.61: 2 residues within 4Å:- Chain P: I.28
- Chain Q: R.33
Ligand excluded by PLIPBME.62: 4 residues within 4Å:- Chain Q: T.21, P.22, D.23, K.193
Ligand excluded by PLIPBME.63: 5 residues within 4Å:- Chain Q: G.57, A.58, H.59, D.60, N.66
Ligand excluded by PLIPBME.75: 6 residues within 4Å:- Chain T: I.171, A.172, R.184, F.185, D.186, R.188
Ligand excluded by PLIPBME.76: 7 residues within 4Å:- Chain T: E.34, I.35, W.36, N.37, R.38, Y.83, L.85
Ligand excluded by PLIPBME.80: 2 residues within 4Å:- Chain V: R.109, P.121
Ligand excluded by PLIPBME.84: 2 residues within 4Å:- Chain V: I.28
- Chain W: R.33
Ligand excluded by PLIPBME.85: 4 residues within 4Å:- Chain W: T.21, P.22, D.23, K.193
Ligand excluded by PLIPBME.86: 5 residues within 4Å:- Chain W: G.57, A.58, H.59, D.60, N.66
Ligand excluded by PLIP- 12 x FE: FE (III) ION(Non-covalent)
FE.12: 5 residues within 4Å:- Chain D: Y.108, R.157, H.160, Y.162
- Ligands: DHB.13
3 PLIP interactions:3 interactions with chain D- Metal complexes: D:Y.108, D:H.160, D:Y.162
FE.18: 4 residues within 4Å:- Chain E: Y.108, H.160, Y.162
- Ligands: DHB.19
3 PLIP interactions:3 interactions with chain E- Metal complexes: E:Y.108, E:H.160, E:Y.162
FE.22: 5 residues within 4Å:- Chain F: Y.108, R.157, H.160, Y.162
- Ligands: DHB.23
3 PLIP interactions:3 interactions with chain F- Metal complexes: F:Y.108, F:H.160, F:Y.162
FE.35: 5 residues within 4Å:- Chain J: Y.108, R.157, H.160, Y.162
- Ligands: DHB.36
3 PLIP interactions:3 interactions with chain J- Metal complexes: J:Y.108, J:H.160, J:Y.162
FE.41: 4 residues within 4Å:- Chain K: Y.108, H.160, Y.162
- Ligands: DHB.42
3 PLIP interactions:3 interactions with chain K- Metal complexes: K:Y.108, K:H.160, K:Y.162
FE.45: 5 residues within 4Å:- Chain L: Y.108, R.157, H.160, Y.162
- Ligands: DHB.46
3 PLIP interactions:3 interactions with chain L- Metal complexes: L:Y.108, L:H.160, L:Y.162
FE.58: 5 residues within 4Å:- Chain P: Y.108, R.157, H.160, Y.162
- Ligands: DHB.59
3 PLIP interactions:3 interactions with chain P- Metal complexes: P:Y.108, P:H.160, P:Y.162
FE.64: 4 residues within 4Å:- Chain Q: Y.108, H.160, Y.162
- Ligands: DHB.65
3 PLIP interactions:3 interactions with chain Q- Metal complexes: Q:Y.108, Q:H.160, Q:Y.162
FE.68: 5 residues within 4Å:- Chain R: Y.108, R.157, H.160, Y.162
- Ligands: DHB.69
3 PLIP interactions:3 interactions with chain R- Metal complexes: R:Y.108, R:H.160, R:Y.162
FE.81: 5 residues within 4Å:- Chain V: Y.108, R.157, H.160, Y.162
- Ligands: DHB.82
3 PLIP interactions:3 interactions with chain V- Metal complexes: V:Y.108, V:H.160, V:Y.162
FE.87: 4 residues within 4Å:- Chain W: Y.108, H.160, Y.162
- Ligands: DHB.88
3 PLIP interactions:3 interactions with chain W- Metal complexes: W:Y.108, W:H.160, W:Y.162
FE.91: 5 residues within 4Å:- Chain X: Y.108, R.157, H.160, Y.162
- Ligands: DHB.92
3 PLIP interactions:3 interactions with chain X- Metal complexes: X:Y.108, X:H.160, X:Y.162
- 12 x DHB: 3,4-DIHYDROXYBENZOIC ACID(Non-covalent)
DHB.13: 9 residues within 4Å:- Chain A: P.15, Y.16
- Chain D: Y.108, H.147, W.149, R.157, H.160, Y.162
- Ligands: FE.12
10 PLIP interactions:7 interactions with chain D, 3 interactions with chain A- Hydrophobic interactions: D:W.149, D:W.149, D:W.149, D:R.157, A:P.15, A:Y.16
- Hydrogen bonds: D:R.157
- Water bridges: D:H.147, A:Y.16
- Salt bridges: D:H.147
DHB.19: 9 residues within 4Å:- Chain B: P.15, Y.16
- Chain E: Y.108, H.147, W.149, R.157, H.160, Y.162
- Ligands: FE.18
8 PLIP interactions:5 interactions with chain E, 3 interactions with chain B- Hydrophobic interactions: E:W.149, E:W.149, E:W.149, E:R.157, B:P.15, B:Y.16
- Hydrogen bonds: E:R.157, B:Y.16
DHB.23: 10 residues within 4Å:- Chain C: P.15, Y.16
- Chain F: Y.108, H.147, W.149, R.157, H.160, Y.162, I.191
- Ligands: FE.22
10 PLIP interactions:4 interactions with chain C, 6 interactions with chain F- Hydrophobic interactions: C:P.15, C:Y.16, F:W.149, F:W.149, F:R.157, F:I.191
- Hydrogen bonds: C:Y.16, F:R.157
- Water bridges: C:R.133, F:R.150
DHB.36: 9 residues within 4Å:- Chain G: P.15, Y.16
- Chain J: Y.108, H.147, W.149, R.157, H.160, Y.162
- Ligands: FE.35
10 PLIP interactions:7 interactions with chain J, 3 interactions with chain G- Hydrophobic interactions: J:W.149, J:W.149, J:W.149, J:R.157, G:P.15, G:Y.16
- Hydrogen bonds: J:R.157
- Water bridges: J:H.147, G:Y.16
- Salt bridges: J:H.147
DHB.42: 9 residues within 4Å:- Chain H: P.15, Y.16
- Chain K: Y.108, H.147, W.149, R.157, H.160, Y.162
- Ligands: FE.41
8 PLIP interactions:3 interactions with chain H, 5 interactions with chain K- Hydrophobic interactions: H:P.15, H:Y.16, K:W.149, K:W.149, K:W.149, K:R.157
- Hydrogen bonds: H:Y.16, K:R.157
DHB.46: 10 residues within 4Å:- Chain I: P.15, Y.16
- Chain L: Y.108, H.147, W.149, R.157, H.160, Y.162, I.191
- Ligands: FE.45
10 PLIP interactions:4 interactions with chain I, 6 interactions with chain L- Hydrophobic interactions: I:P.15, I:Y.16, L:W.149, L:W.149, L:R.157, L:I.191
- Hydrogen bonds: I:Y.16, L:R.157
- Water bridges: I:R.133, L:R.150
DHB.59: 9 residues within 4Å:- Chain M: P.15, Y.16
- Chain P: Y.108, H.147, W.149, R.157, H.160, Y.162
- Ligands: FE.58
11 PLIP interactions:4 interactions with chain M, 7 interactions with chain P- Hydrophobic interactions: M:P.15, M:Y.16, P:W.149, P:W.149, P:W.149, P:R.157
- Hydrogen bonds: M:Y.16, P:R.157
- Water bridges: M:Y.16, P:H.147
- Salt bridges: P:H.147
DHB.65: 9 residues within 4Å:- Chain N: P.15, Y.16
- Chain Q: Y.108, H.147, W.149, R.157, H.160, Y.162
- Ligands: FE.64
9 PLIP interactions:4 interactions with chain N, 5 interactions with chain Q- Hydrophobic interactions: N:P.15, N:Y.16, Q:W.149, Q:W.149, Q:W.149, Q:R.157
- Hydrogen bonds: N:Y.16, Q:R.157
- Water bridges: N:Y.16
DHB.69: 10 residues within 4Å:- Chain O: P.15, Y.16
- Chain R: Y.108, H.147, W.149, R.157, H.160, Y.162, I.191
- Ligands: FE.68
11 PLIP interactions:6 interactions with chain R, 5 interactions with chain O- Hydrophobic interactions: R:W.149, R:W.149, R:R.157, R:I.191, O:P.15, O:Y.16
- Hydrogen bonds: R:R.157, O:Y.16, O:Y.16
- Water bridges: R:R.150, O:R.133
DHB.82: 9 residues within 4Å:- Chain S: P.15, Y.16
- Chain V: Y.108, H.147, W.149, R.157, H.160, Y.162
- Ligands: FE.81
11 PLIP interactions:4 interactions with chain S, 7 interactions with chain V- Hydrophobic interactions: S:P.15, S:Y.16, V:W.149, V:W.149, V:W.149, V:R.157
- Hydrogen bonds: S:Y.16, V:R.157
- Water bridges: S:Y.16, V:H.147
- Salt bridges: V:H.147
DHB.88: 9 residues within 4Å:- Chain T: P.15, Y.16
- Chain W: Y.108, H.147, W.149, R.157, H.160, Y.162
- Ligands: FE.87
9 PLIP interactions:5 interactions with chain W, 4 interactions with chain T- Hydrophobic interactions: W:W.149, W:W.149, W:W.149, W:R.157, T:P.15, T:Y.16
- Hydrogen bonds: W:R.157, T:Y.16
- Water bridges: T:Y.16
DHB.92: 10 residues within 4Å:- Chain U: P.15, Y.16
- Chain X: Y.108, H.147, W.149, R.157, H.160, Y.162, I.191
- Ligands: FE.91
11 PLIP interactions:5 interactions with chain U, 6 interactions with chain X- Hydrophobic interactions: U:P.15, U:Y.16, X:W.149, X:W.149, X:R.157, X:I.191
- Hydrogen bonds: U:Y.16, U:Y.16, X:R.157
- Water bridges: U:R.133, X:R.150
- 4 x CL: CHLORIDE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Purpero, V.M. et al., Axial Ligand Swapping In Double Mutant Maintains Intradiol-cleavage Chemistry in Protocatechuate 3,4-Dioxygenase. To be Published
- Release Date
- 2011-06-01
- 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
BC
CG
AH
BI
CM
AN
BO
CS
AT
BU
CD
ME
NF
OJ
MK
NL
OP
MQ
NR
OV
MW
NX
O
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.86 Å
- Oligo State
- hetero-12-12-mer
- Ligands
- 28 x SO4: SULFATE ION(Non-functional Binders)
- 12 x GOL: GLYCEROL(Non-functional Binders)
- 24 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)
- 12 x FE: FE (III) ION(Non-covalent)
- 12 x DHB: 3,4-DIHYDROXYBENZOIC ACID(Non-covalent)
- 4 x CL: CHLORIDE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Purpero, V.M. et al., Axial Ligand Swapping In Double Mutant Maintains Intradiol-cleavage Chemistry in Protocatechuate 3,4-Dioxygenase. To be Published
- Release Date
- 2011-06-01
- 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
BC
CG
AH
BI
CM
AN
BO
CS
AT
BU
CD
ME
NF
OJ
MK
NL
OP
MQ
NR
OV
MW
NX
O