SMTL ID : 3pcb.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.19 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: 3HB.2 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:Y.108, B:Y.147, B:H.160, B:H.162 FE.4: 5 residues within 4Å: Chain D: Y.108, Y.147, H.160, H.162 Ligands: 3HB.5 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:Y.108, D:Y.147, D:H.160, D:H.162 FE.7: 5 residues within 4Å: Chain F: Y.108, Y.147, H.160, H.162 Ligands: 3HB.8 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:Y.108, F:Y.147, F:H.160, F:H.162 FE.10: 5 residues within 4Å: Chain H: Y.108, Y.147, H.160, H.162 Ligands: 3HB.11 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:Y.108, H:Y.147, H:H.160, H:H.162 FE.13: 5 residues within 4Å: Chain J: Y.108, Y.147, H.160, H.162 Ligands: 3HB.14 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:Y.108, J:Y.147, J:H.160, J:H.162 FE.16: 5 residues within 4Å: Chain L: Y.108, Y.147, H.160, H.162 Ligands: 3HB.17 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:Y.108, L:Y.147, L:H.160, L:H.162 FE.19: 5 residues within 4Å: Chain N: Y.108, Y.147, H.160, H.162 Ligands: 3HB.20 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:Y.108, N:Y.147, N:H.160, N:H.162 FE.22: 5 residues within 4Å: Chain P: Y.108, Y.147, H.160, H.162 Ligands: 3HB.23 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:Y.108, P:Y.147, P:H.160, P:H.162 FE.25: 5 residues within 4Å: Chain R: Y.108, Y.147, H.160, H.162 Ligands: 3HB.26 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:Y.108, R:Y.147, R:H.160, R:H.162 FE.28: 5 residues within 4Å: Chain T: Y.108, Y.147, H.160, H.162 Ligands: 3HB.29 4 PLIP interactions: 4 interactions with chain T Metal complexes: T:Y.108, T:Y.147, T:H.160, T:H.162 FE.31: 5 residues within 4Å: Chain V: Y.108, Y.147, H.160, H.162 Ligands: 3HB.32 4 PLIP interactions: 4 interactions with chain V Metal complexes: V:Y.108, V:Y.147, V:H.160, V:H.162 FE.34: 5 residues within 4Å: Chain X: Y.108, Y.147, H.160, H.162 Ligands: 3HB.35 4 PLIP interactions: 4 interactions with chain X Metal complexes: X:Y.108, X:Y.147, X:H.160, X:H.162

24 x 3HB: 3-HYDROXYBENZOIC ACID(Non-functional Binders)(Non-covalent)

3HB.2: 11 residues within 4Å: Chain A: G.14, P.15, R.133 Chain B: Y.24, Y.147, W.149, R.157, H.162, Q.177, I.191 Ligands: FE.1 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:P.15, B:Y.147, B:W.149, B:R.157, B:I.191 Hydrogen bonds: B:R.157, B:Q.177 3HB.3: 4 residues within 4Å: Chain B: L.20, R.33 Chain F: L.20, P.22 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.20 pi-Cation interactions: B:R.33 3HB.5: 12 residues within 4Å: Chain C: G.14, P.15, R.133 Chain D: Y.24, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.4 9 PLIP interactions: 7 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:Y.147, D:W.149, D:R.157, D:I.191, C:P.15 Hydrogen bonds: D:Y.24, D:R.157, D:Q.177, C:G.134 3HB.6: 4 residues within 4Å: Chain B: P.22, I.28 Chain D: L.20, R.33 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: B:P.22, B:I.28, D:L.20 Water bridges: D:L.20 pi-Cation interactions: D:R.33 3HB.8: 12 residues within 4Å: Chain E: G.14, P.15, R.133, G.134 Chain F: Y.24, Y.147, W.149, R.157, H.162, Q.177, I.191 Ligands: FE.7 9 PLIP interactions: 3 interactions with chain E, 6 interactions with chain F Hydrophobic interactions: E:P.15, F:Y.147, F:W.149, F:R.157, F:I.191 Hydrogen bonds: E:G.134, F:R.157, F:Q.177 Salt bridges: E:R.133 3HB.9: 4 residues within 4Å: Chain D: P.22, I.28 Chain F: L.20, R.33 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain D Hydrophobic interactions: F:L.20, D:P.22, D:I.28 pi-Cation interactions: F:R.33 3HB.11: 12 residues within 4Å: Chain G: G.14, P.15, R.133 Chain H: Y.24, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.10 8 PLIP interactions: 2 interactions with chain G, 6 interactions with chain H Hydrophobic interactions: G:P.15, H:Y.147, H:W.149, H:R.157, H:I.191 Hydrogen bonds: G:G.134, H:R.157, H:Q.177 3HB.12: 3 residues within 4Å: Chain H: R.33 Chain L: P.22, I.28 3 PLIP interactions: 2 interactions with chain L, 1 interactions with chain H Hydrophobic interactions: L:P.22, L:I.28 Water bridges: H:L.20 3HB.14: 11 residues within 4Å: Chain I: G.14, P.15, R.133 Chain J: Y.24, Y.147, W.149, R.157, H.162, Q.177, I.191 Ligands: FE.13 9 PLIP interactions: 7 interactions with chain J, 2 interactions with chain I Hydrophobic interactions: J:Y.147, J:W.149, J:R.157, J:I.191, I:P.15 Hydrogen bonds: J:Y.24, J:R.157, J:Q.177 Salt bridges: I:R.133 3HB.15: 4 residues within 4Å: Chain H: L.20, P.22, I.28 Chain J: R.33 3 PLIP interactions: 1 interactions with chain J, 2 interactions with chain H pi-Cation interactions: J:R.33 Hydrophobic interactions: H:P.22, H:I.28 3HB.17: 13 residues within 4Å: Chain K: G.14, P.15, R.133, G.134 Chain L: Y.24, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.16 8 PLIP interactions: 2 interactions with chain K, 6 interactions with chain L Hydrophobic interactions: K:P.15, L:Y.147, L:W.149, L:R.157, L:I.191 Hydrogen bonds: K:G.134, L:R.157, L:Q.177 3HB.18: 5 residues within 4Å: Chain J: L.20, P.22, I.28 Chain L: L.20, R.33 4 PLIP interactions: 3 interactions with chain J, 1 interactions with chain L Hydrophobic interactions: J:P.22, J:P.22, J:I.28 pi-Cation interactions: L:R.33 3HB.20: 11 residues within 4Å: Chain M: G.14, P.15, R.133 Chain N: Y.24, Y.147, W.149, R.157, H.162, Q.177, I.191 Ligands: FE.19 8 PLIP interactions: 7 interactions with chain N, 1 interactions with chain M Hydrophobic interactions: N:Y.147, N:W.149, N:R.157, N:I.191, M:P.15 Hydrogen bonds: N:Y.24, N:R.157, N:Q.177 3HB.21: 4 residues within 4Å: Chain N: L.20, R.33 Chain R: L.20, P.22 2 PLIP interactions: 2 interactions with chain N Hydrophobic interactions: N:L.20 pi-Cation interactions: N:R.33 3HB.23: 12 residues within 4Å: Chain O: G.14, P.15, R.133 Chain P: Y.24, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.22 8 PLIP interactions: 2 interactions with chain O, 6 interactions with chain P Hydrophobic interactions: O:P.15, P:Y.147, P:W.149, P:R.157, P:I.191 Hydrogen bonds: O:G.134, P:R.157, P:Q.177 3HB.24: 4 residues within 4Å: Chain N: P.22, I.28 Chain P: L.20, R.33 5 PLIP interactions: 2 interactions with chain N, 3 interactions with chain P Hydrophobic interactions: N:P.22, N:I.28, P:L.20 Water bridges: P:L.20 pi-Cation interactions: P:R.33 3HB.26: 12 residues within 4Å: Chain Q: G.14, P.15, R.133, G.134 Chain R: Y.24, Y.147, W.149, R.157, H.162, Q.177, I.191 Ligands: FE.25 10 PLIP interactions: 7 interactions with chain R, 3 interactions with chain Q Hydrophobic interactions: R:Y.147, R:W.149, R:R.157, R:I.191, Q:P.15 Hydrogen bonds: R:Y.24, R:R.157, R:Q.177, Q:G.134 Salt bridges: Q:R.133 3HB.27: 4 residues within 4Å: Chain P: P.22, I.28 Chain R: L.20, R.33 4 PLIP interactions: 2 interactions with chain P, 2 interactions with chain R Hydrophobic interactions: P:P.22, P:I.28, R:L.20 pi-Cation interactions: R:R.33 3HB.29: 12 residues within 4Å: Chain S: G.14, P.15, R.133 Chain T: Y.24, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.28 9 PLIP interactions: 2 interactions with chain S, 7 interactions with chain T Hydrophobic interactions: S:P.15, T:Y.147, T:W.149, T:R.157, T:I.191 Hydrogen bonds: S:G.134, T:Y.24, T:R.157, T:Q.177 3HB.30: 3 residues within 4Å: Chain T: R.33 Chain X: P.22, I.28 3 PLIP interactions: 2 interactions with chain X, 1 interactions with chain T Hydrophobic interactions: X:P.22, X:I.28 Water bridges: T:L.20 3HB.32: 11 residues within 4Å: Chain U: G.14, P.15, R.133 Chain V: Y.24, Y.147, W.149, R.157, H.162, Q.177, I.191 Ligands: FE.31 8 PLIP interactions: 6 interactions with chain V, 2 interactions with chain U Hydrophobic interactions: V:Y.147, V:W.149, V:R.157, V:I.191, U:P.15 Hydrogen bonds: V:R.157, V:Q.177 Salt bridges: U:R.133 3HB.33: 4 residues within 4Å: Chain T: L.20, P.22, I.28 Chain V: R.33 3 PLIP interactions: 1 interactions with chain V, 2 interactions with chain T pi-Cation interactions: V:R.33 Hydrophobic interactions: T:P.22, T:I.28 3HB.35: 13 residues within 4Å: Chain W: G.14, P.15, R.133, G.134 Chain X: Y.24, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.34 9 PLIP interactions: 7 interactions with chain X, 2 interactions with chain W Hydrophobic interactions: X:Y.147, X:W.149, X:R.157, X:I.191, W:P.15 Hydrogen bonds: X:Y.24, X:R.157, X:Q.177, W:G.134 3HB.36: 5 residues within 4Å: Chain V: L.20, P.22, I.28 Chain X: L.20, R.33 4 PLIP interactions: 3 interactions with chain V, 1 interactions with chain X Hydrophobic interactions: V:P.22, V:P.22, V:I.28 pi-Cation interactions: X: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

1998-04-29

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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