SMTL ID : 3pch.1

STRUCTURE OF PROTOCATECHUATE 3,4-DIOXYGENASE COMPLEXED WITH 3-CHLORO-4-HYDROXYBENZOATE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

hetero-12-12-mer

Ligands

12 x FE: FE (III) ION(Non-covalent)(Non-functional Binders)

FE.1: 5 residues within 4Å: Chain B: Y.108, Y.147, H.160, H.162 Ligands: CHB.2 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:Y.108, B:Y.147, B:H.160, B:H.162, H2O.9 FE.4: 5 residues within 4Å: Chain D: Y.108, Y.147, H.160, H.162 Ligands: CHB.5 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.19 FE.7: 5 residues within 4Å: Chain F: Y.108, Y.147, H.160, H.162 Ligands: CHB.8 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.28 FE.10: 5 residues within 4Å: Chain H: Y.108, Y.147, H.160, H.162 Ligands: CHB.11 5 PLIP interactions: 4 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:Y.108, H:Y.147, H:H.160, H:H.162, H2O.37 FE.13: 5 residues within 4Å: Chain J: Y.108, Y.147, H.160, H.162 Ligands: CHB.14 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.47 FE.16: 5 residues within 4Å: Chain L: Y.108, Y.147, H.160, H.162 Ligands: CHB.17 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.56 FE.19: 5 residues within 4Å: Chain N: Y.108, Y.147, H.160, H.162 Ligands: CHB.20 5 PLIP interactions: 4 interactions with chain N, 1 Ligand-Water interactions Metal complexes: N:Y.108, N:Y.147, N:H.160, N:H.162, H2O.65 FE.22: 5 residues within 4Å: Chain P: Y.108, Y.147, H.160, H.162 Ligands: CHB.23 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.75 FE.25: 5 residues within 4Å: Chain R: Y.108, Y.147, H.160, H.162 Ligands: CHB.26 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.84 FE.28: 5 residues within 4Å: Chain T: Y.108, Y.147, H.160, H.162 Ligands: CHB.29 5 PLIP interactions: 4 interactions with chain T, 1 Ligand-Water interactions Metal complexes: T:Y.108, T:Y.147, T:H.160, T:H.162, H2O.93 FE.31: 5 residues within 4Å: Chain V: Y.108, Y.147, H.160, H.162 Ligands: CHB.32 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.103 FE.34: 5 residues within 4Å: Chain X: Y.108, Y.147, H.160, H.162 Ligands: CHB.35 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.112

24 x CHB: 3-CHLORO-4-HYDROXYBENZOIC ACID(Non-functional Binders)(Non-covalent)

CHB.2: 14 residues within 4Å: Chain A: T.12, G.14, P.15, R.133 Chain B: Y.24, Y.108, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.1 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.147, B:W.149, B:I.191, A:P.15 Hydrogen bonds: B:R.157 Halogen bonds: B:Q.177 Salt bridges: A:R.133 CHB.3: 4 residues within 4Å: Chain B: L.20, R.33 Chain F: P.22, I.28 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain F Hydrophobic interactions: B:L.20, F:P.22 pi-Cation interactions: B:R.33 Water bridges: F:R.33 CHB.5: 14 residues within 4Å: Chain C: T.12, G.14, P.15, R.133 Chain D: Y.24, Y.108, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.4 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:Y.147, D:W.149, D:I.191, C:P.15 Hydrogen bonds: D:Y.24, D:R.157 Halogen bonds: D:Q.177 Salt bridges: C:R.133 CHB.6: 6 residues within 4Å: Chain B: L.20, P.22, I.28, R.33 Chain D: L.20, R.33 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:P.22, D:L.20 Water bridges: B:R.33 pi-Cation interactions: D:R.33 CHB.8: 14 residues within 4Å: Chain E: T.12, G.14, P.15, R.133 Chain F: Y.24, Y.108, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.7 7 PLIP interactions: 5 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:Y.147, F:W.149, F:I.191, E:P.15 Hydrogen bonds: F:R.157 Halogen bonds: F:Q.177 Salt bridges: E:R.133 CHB.9: 4 residues within 4Å: Chain D: P.22, I.28 Chain F: L.20, R.33 4 PLIP interactions: 1 interactions with chain F, 3 interactions with chain D Hydrophobic interactions: F:L.20, D:P.22, D:P.22 Water bridges: D:R.33 CHB.11: 14 residues within 4Å: Chain G: T.12, G.14, P.15, R.133 Chain H: Y.24, Y.108, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.10 8 PLIP interactions: 6 interactions with chain H, 2 interactions with chain G Hydrophobic interactions: H:Y.147, H:W.149, H:R.157, H:I.191, G:P.15 Hydrogen bonds: H:R.157 Halogen bonds: H:Q.177 Salt bridges: G:R.133 CHB.12: 5 residues within 4Å: Chain H: L.20, R.33 Chain L: P.22, I.28, R.33 4 PLIP interactions: 2 interactions with chain H, 2 interactions with chain L Hydrophobic interactions: H:L.20, L:P.22, L:I.28 pi-Cation interactions: H:R.33 CHB.14: 14 residues within 4Å: Chain I: T.12, G.14, P.15, R.133 Chain J: Y.24, Y.108, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.13 8 PLIP interactions: 6 interactions with chain J, 2 interactions with chain I Hydrophobic interactions: J:Y.147, J:W.149, J:I.191, I:P.15 Hydrogen bonds: J:Y.24, J:R.157 Halogen bonds: J:Q.177 Salt bridges: I:R.133 CHB.15: 4 residues within 4Å: Chain H: P.22, I.28 Chain J: L.20, R.33 5 PLIP interactions: 3 interactions with chain H, 2 interactions with chain J Hydrophobic interactions: H:P.22, H:P.22, J:L.20 Water bridges: H:R.33 pi-Cation interactions: J:R.33 CHB.17: 14 residues within 4Å: Chain K: T.12, G.14, P.15, R.133 Chain L: Y.24, Y.108, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.16 8 PLIP interactions: 6 interactions with chain L, 2 interactions with chain K Hydrophobic interactions: L:Y.147, L:W.149, L:R.157, L:I.191, K:P.15 Hydrogen bonds: L:R.157 Halogen bonds: L:Q.177 Salt bridges: K:R.133 CHB.18: 4 residues within 4Å: Chain J: L.20, P.22, I.28 Chain L: R.33 4 PLIP interactions: 4 interactions with chain J Hydrophobic interactions: J:P.22, J:P.22, J:I.28 Water bridges: J:R.33 CHB.20: 14 residues within 4Å: Chain M: T.12, G.14, P.15, R.133 Chain N: Y.24, Y.108, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.19 8 PLIP interactions: 2 interactions with chain M, 6 interactions with chain N Hydrophobic interactions: M:P.15, N:Y.147, N:W.149, N:I.191 Salt bridges: M:R.133 Hydrogen bonds: N:Y.24, N:R.157 Halogen bonds: N:Q.177 CHB.21: 4 residues within 4Å: Chain N: L.20, R.33 Chain R: P.22, I.28 4 PLIP interactions: 2 interactions with chain R, 2 interactions with chain N Hydrophobic interactions: R:P.22, N:L.20 Water bridges: R:R.33 pi-Cation interactions: N:R.33 CHB.23: 14 residues within 4Å: Chain O: T.12, G.14, P.15, R.133 Chain P: Y.24, Y.108, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.22 7 PLIP interactions: 5 interactions with chain P, 2 interactions with chain O Hydrophobic interactions: P:Y.147, P:W.149, P:I.191, O:P.15 Hydrogen bonds: P:R.157 Halogen bonds: P:Q.177 Salt bridges: O:R.133 CHB.24: 6 residues within 4Å: Chain N: L.20, P.22, I.28, R.33 Chain P: L.20, R.33 4 PLIP interactions: 2 interactions with chain P, 2 interactions with chain N Hydrophobic interactions: P:L.20, N:P.22 pi-Cation interactions: P:R.33 Water bridges: N:R.33 CHB.26: 14 residues within 4Å: Chain Q: T.12, G.14, P.15, R.133 Chain R: Y.24, Y.108, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.25 8 PLIP interactions: 6 interactions with chain R, 2 interactions with chain Q Hydrophobic interactions: R:Y.147, R:W.149, R:I.191, Q:P.15 Hydrogen bonds: R:Y.24, R:R.157 Halogen bonds: R:Q.177 Salt bridges: Q:R.133 CHB.27: 4 residues within 4Å: Chain P: P.22, I.28 Chain R: L.20, R.33 4 PLIP interactions: 1 interactions with chain R, 3 interactions with chain P Hydrophobic interactions: R:L.20, P:P.22, P:P.22 Water bridges: P:R.33 CHB.29: 14 residues within 4Å: Chain S: T.12, G.14, P.15, R.133 Chain T: Y.24, Y.108, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.28 9 PLIP interactions: 7 interactions with chain T, 2 interactions with chain S Hydrophobic interactions: T:Y.147, T:W.149, T:R.157, T:I.191, S:P.15 Hydrogen bonds: T:Y.24, T:R.157 Halogen bonds: T:Q.177 Salt bridges: S:R.133 CHB.30: 5 residues within 4Å: Chain T: L.20, R.33 Chain X: P.22, I.28, R.33 4 PLIP interactions: 2 interactions with chain T, 2 interactions with chain X Hydrophobic interactions: T:L.20, X:P.22, X:I.28 pi-Cation interactions: T:R.33 CHB.32: 14 residues within 4Å: Chain U: T.12, G.14, P.15, R.133 Chain V: Y.24, Y.108, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.31 7 PLIP interactions: 2 interactions with chain U, 5 interactions with chain V Hydrophobic interactions: U:P.15, V:Y.147, V:W.149, V:I.191 Salt bridges: U:R.133 Hydrogen bonds: V:R.157 Halogen bonds: V:Q.177 CHB.33: 4 residues within 4Å: Chain T: P.22, I.28 Chain V: L.20, R.33 5 PLIP interactions: 2 interactions with chain V, 3 interactions with chain T Hydrophobic interactions: V:L.20, T:P.22, T:P.22 pi-Cation interactions: V:R.33 Water bridges: T:R.33 CHB.35: 14 residues within 4Å: Chain W: T.12, G.14, P.15, R.133 Chain X: Y.24, Y.108, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.34 9 PLIP interactions: 2 interactions with chain W, 7 interactions with chain X Hydrophobic interactions: W:P.15, X:Y.147, X:W.149, X:R.157, X:I.191 Salt bridges: W:R.133 Hydrogen bonds: X:Y.24, X:R.157 Halogen bonds: X:Q.177 CHB.36: 4 residues within 4Å: Chain V: L.20, P.22, I.28 Chain X: R.33 4 PLIP interactions: 4 interactions with chain V Hydrophobic interactions: V:P.22, V:P.22, V:I.28 Water bridges: V:R.33

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Orville, A.M. et al., Structures of competitive inhibitor complexes of protocatechuate 3,4-dioxygenase: multiple exogenous ligand binding orientations within the active site. Biochemistry (1997)

Release Date

1998-01-07

Peptides

Protocatechuate 3,4-dioxygenase alpha chain: ACEGIKMOQSUW
Protocatechuate 3,4-dioxygenase beta chain: BDFHJLNPRTVX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

E
C

G
D

I
E

K
F

M
A

O
B

Q
C

S
D

U
E

W
F

B
M

D
N

F
O

H
P

J
Q

L
R

N
M

P
N

R
O

T
P

V
Q

X
R

Protocatechuate 3,4-dioxygenase alpha chain

Protocatechuate 3,4-dioxygenase beta chain

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