SMTL ID : 3pcn.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-12-12-mer

Ligands

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

FE.1: 4 residues within 4Å: Chain B: Y.108, H.160, H.162 Ligands: DHY.3 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:Y.108, B:H.160, B:H.162 FE.4: 4 residues within 4Å: Chain D: Y.108, H.160, H.162 Ligands: DHY.6 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:Y.108, D:H.160, D:H.162 FE.7: 4 residues within 4Å: Chain F: Y.108, H.160, H.162 Ligands: DHY.9 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:Y.108, F:H.160, F:H.162 FE.10: 4 residues within 4Å: Chain H: Y.108, H.160, H.162 Ligands: DHY.12 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:Y.108, H:H.160, H:H.162 FE.13: 4 residues within 4Å: Chain J: Y.108, H.160, H.162 Ligands: DHY.15 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:Y.108, J:H.160, J:H.162 FE.16: 4 residues within 4Å: Chain L: Y.108, H.160, H.162 Ligands: DHY.18 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:Y.108, L:H.160, L:H.162 FE.19: 4 residues within 4Å: Chain N: Y.108, H.160, H.162 Ligands: DHY.21 3 PLIP interactions: 3 interactions with chain N Metal complexes: N:Y.108, N:H.160, N:H.162 FE.22: 4 residues within 4Å: Chain P: Y.108, H.160, H.162 Ligands: DHY.24 3 PLIP interactions: 3 interactions with chain P Metal complexes: P:Y.108, P:H.160, P:H.162 FE.25: 4 residues within 4Å: Chain R: Y.108, H.160, H.162 Ligands: DHY.27 3 PLIP interactions: 3 interactions with chain R Metal complexes: R:Y.108, R:H.160, R:H.162 FE.28: 4 residues within 4Å: Chain T: Y.108, H.160, H.162 Ligands: DHY.30 3 PLIP interactions: 3 interactions with chain T Metal complexes: T:Y.108, T:H.160, T:H.162 FE.31: 4 residues within 4Å: Chain V: Y.108, H.160, H.162 Ligands: DHY.33 3 PLIP interactions: 3 interactions with chain V Metal complexes: V:Y.108, V:H.160, V:H.162 FE.34: 4 residues within 4Å: Chain X: Y.108, H.160, H.162 Ligands: DHY.36 3 PLIP interactions: 3 interactions with chain X Metal complexes: X:Y.108, X:H.160, X:H.162

12 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.2: 4 residues within 4Å: Chain B: H.61, C.129, L.130, S.138 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.138 BME.5: 4 residues within 4Å: Chain D: H.61, C.129, L.130, S.138 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.138 BME.8: 4 residues within 4Å: Chain F: H.61, C.129, L.130, S.138 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:S.138 BME.11: 4 residues within 4Å: Chain H: H.61, C.129, L.130, S.138 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:S.138 BME.14: 4 residues within 4Å: Chain J: H.61, C.129, L.130, S.138 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:S.138 BME.17: 5 residues within 4Å: Chain L: H.61, C.129, L.130, Y.137, S.138 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:S.138 BME.20: 4 residues within 4Å: Chain N: H.61, C.129, L.130, S.138 1 PLIP interactions: 1 interactions with chain N Hydrogen bonds: N:S.138 BME.23: 4 residues within 4Å: Chain P: H.61, C.129, L.130, S.138 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:S.138 BME.26: 4 residues within 4Å: Chain R: H.61, C.129, L.130, S.138 1 PLIP interactions: 1 interactions with chain R Hydrogen bonds: R:S.138 BME.29: 4 residues within 4Å: Chain T: H.61, C.129, L.130, S.138 1 PLIP interactions: 1 interactions with chain T Hydrogen bonds: T:S.138 BME.32: 4 residues within 4Å: Chain V: H.61, C.129, L.130, S.138 1 PLIP interactions: 1 interactions with chain V Hydrogen bonds: V:S.138 BME.35: 5 residues within 4Å: Chain X: H.61, C.129, L.130, Y.137, S.138 1 PLIP interactions: 1 interactions with chain X Hydrogen bonds: X:S.138

12 x DHY: 2-(3,4-DIHYDROXYPHENYL)ACETIC ACID(Non-covalent)

DHY.3: 13 residues within 4Å: Chain A: P.15, Y.16, 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: 3 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:P.15, A:Y.16, B:Y.147, B:W.149, B:I.191 Water bridges: A:Y.16 Hydrogen bonds: B:R.157 DHY.6: 12 residues within 4Å: Chain C: P.15, Y.16, R.133 Chain D: Y.24, Y.108, Y.147, W.149, R.157, H.160, H.162, I.191 Ligands: FE.4 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:Y.147, D:W.149, D:I.191, C:Y.16 Hydrogen bonds: D:Y.24, D:R.157 Water bridges: C:Y.16 DHY.9: 12 residues within 4Å: Chain E: P.15, Y.16, R.133 Chain F: Y.24, Y.108, Y.147, W.149, R.157, H.160, H.162, I.191 Ligands: FE.7 7 PLIP interactions: 3 interactions with chain E, 4 interactions with chain F Hydrophobic interactions: E:P.15, E:Y.16, F:Y.147, F:W.149, F:I.191 Water bridges: E:Y.16 Hydrogen bonds: F:R.157 DHY.12: 13 residues within 4Å: Chain G: P.15, Y.16, 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 7 PLIP interactions: 3 interactions with chain G, 4 interactions with chain H Hydrophobic interactions: G:P.15, G:Y.16, H:Y.147, H:W.149, H:I.191 Water bridges: G:Y.16 Hydrogen bonds: H:R.157 DHY.15: 13 residues within 4Å: Chain I: P.15, Y.16, 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 10 PLIP interactions: 8 interactions with chain J, 2 interactions with chain I Hydrophobic interactions: J:Y.24, J:Y.147, J:W.149, J:I.191, I:P.15 Hydrogen bonds: J:Y.24, J:R.157, J:Q.177, J:Q.177 Water bridges: I:Y.16 DHY.18: 13 residues within 4Å: Chain K: P.15, Y.16, 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 7 PLIP interactions: 3 interactions with chain K, 4 interactions with chain L Hydrophobic interactions: K:P.15, K:Y.16, L:Y.147, L:W.149, L:I.191 Water bridges: K:Y.16 Hydrogen bonds: L:R.157 DHY.21: 13 residues within 4Å: Chain M: P.15, Y.16, 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: 5 interactions with chain N, 3 interactions with chain M Hydrophobic interactions: N:Y.147, N:W.149, N:I.191, M:P.15, M:Y.16 Hydrogen bonds: N:Y.24, N:R.157 Water bridges: M:Y.16 DHY.24: 12 residues within 4Å: Chain O: P.15, Y.16, R.133 Chain P: Y.24, Y.108, Y.147, W.149, R.157, H.160, H.162, I.191 Ligands: FE.22 6 PLIP interactions: 4 interactions with chain P, 2 interactions with chain O Hydrophobic interactions: P:Y.147, P:W.149, P:I.191, O:Y.16 Hydrogen bonds: P:R.157 Water bridges: O:Y.16 DHY.27: 12 residues within 4Å: Chain Q: P.15, Y.16, R.133 Chain R: Y.24, Y.108, Y.147, W.149, R.157, H.160, H.162, I.191 Ligands: FE.25 8 PLIP interactions: 3 interactions with chain Q, 5 interactions with chain R Hydrophobic interactions: Q:P.15, Q:Y.16, R:Y.147, R:W.149, R:I.191 Water bridges: Q:Y.16 Hydrogen bonds: R:Y.24, R:R.157 DHY.30: 13 residues within 4Å: Chain S: P.15, Y.16, 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 8 PLIP interactions: 5 interactions with chain T, 3 interactions with chain S Hydrophobic interactions: T:Y.147, T:W.149, T:I.191, S:P.15, S:Y.16 Hydrogen bonds: T:Y.24, T:R.157 Water bridges: S:Y.16 DHY.33: 13 residues within 4Å: Chain U: P.15, Y.16, 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 9 PLIP interactions: 2 interactions with chain U, 7 interactions with chain V Hydrophobic interactions: U:P.15, V:Y.24, V:Y.147, V:W.149, V:I.191 Water bridges: U:Y.16 Hydrogen bonds: V:R.157, V:Q.177, V:Q.177 DHY.36: 13 residues within 4Å: Chain W: P.15, Y.16, 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 8 PLIP interactions: 5 interactions with chain X, 3 interactions with chain W Hydrophobic interactions: X:Y.147, X:W.149, X:I.191, W:P.15, W:Y.16 Hydrogen bonds: X:Y.24, X:R.157 Water bridges: W:Y.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Elgren, T.E. et al., Crystal structure and resonance Raman studies of protocatechuate 3,4-dioxygenase complexed with 3,4-dihydroxyphenylacetate. Biochemistry (1997)

Release Date

1998-02-25

Peptides

PROTOCATECHUATE 3,4-DIOXYGENASE: ACEGIKMOQSUW
PROTOCATECHUATE 3,4-DIOXYGENASE: 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

PROTOCATECHUATE 3,4-DIOXYGENASE

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