SMTL ID : 1eoc.1

CRYSTAL STRUCTURE OF ACINETOBACTER SP. ADP1 PROTOCATECHUATE 3,4-DIOXYGENASE IN COMPLEX WITH 4-NITROCATECHOL

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 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.109, H.161, H.163 Ligands: 4NC.2 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:Y.109, B:H.161, B:H.163, H2O.3 FE.3: 4 residues within 4Å: Chain D: Y.109, H.161, H.163 Ligands: 4NC.4 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:Y.109, D:H.161, D:H.163, H2O.10 FE.5: 4 residues within 4Å: Chain F: Y.109, H.161, H.163 Ligands: 4NC.6 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:Y.109, F:H.161, F:H.163, H2O.18 FE.7: 4 residues within 4Å: Chain H: Y.109, H.161, H.163 Ligands: 4NC.8 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:Y.109, H:H.161, H:H.163, H2O.25 FE.9: 4 residues within 4Å: Chain J: Y.109, H.161, H.163 Ligands: 4NC.10 4 PLIP interactions: 3 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:Y.109, J:H.161, J:H.163, H2O.32 FE.11: 4 residues within 4Å: Chain L: Y.109, H.161, H.163 Ligands: 4NC.12 4 PLIP interactions: 3 interactions with chain L, 1 Ligand-Water interactions Metal complexes: L:Y.109, L:H.161, L:H.163, H2O.39 FE.13: 4 residues within 4Å: Chain N: Y.109, H.161, H.163 Ligands: 4NC.14 4 PLIP interactions: 3 interactions with chain N, 1 Ligand-Water interactions Metal complexes: N:Y.109, N:H.161, N:H.163, H2O.46 FE.15: 4 residues within 4Å: Chain P: Y.109, H.161, H.163 Ligands: 4NC.16 4 PLIP interactions: 3 interactions with chain P, 1 Ligand-Water interactions Metal complexes: P:Y.109, P:H.161, P:H.163, H2O.53 FE.17: 4 residues within 4Å: Chain R: Y.109, H.161, H.163 Ligands: 4NC.18 4 PLIP interactions: 3 interactions with chain R, 1 Ligand-Water interactions Metal complexes: R:Y.109, R:H.161, R:H.163, H2O.60 FE.19: 4 residues within 4Å: Chain T: Y.109, H.161, H.163 Ligands: 4NC.20 4 PLIP interactions: 3 interactions with chain T, 1 Ligand-Water interactions Metal complexes: T:Y.109, T:H.161, T:H.163, H2O.68 FE.21: 4 residues within 4Å: Chain V: Y.109, H.161, H.163 Ligands: 4NC.22 4 PLIP interactions: 3 interactions with chain V, 1 Ligand-Water interactions Metal complexes: V:Y.109, V:H.161, V:H.163, H2O.75 FE.23: 4 residues within 4Å: Chain X: Y.109, H.161, H.163 Ligands: 4NC.24 4 PLIP interactions: 3 interactions with chain X, 1 Ligand-Water interactions Metal complexes: X:Y.109, X:H.161, X:H.163, H2O.82

12 x 4NC: 4-NITROCATECHOL(Non-covalent)

4NC.2: 14 residues within 4Å: Chain A: T.16, G.18, P.19, R.142 Chain B: Y.25, Y.109, Y.148, W.150, R.158, H.161, H.163, Q.178, I.192 Ligands: FE.1 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.148, B:W.150, B:R.158, B:I.192, A:P.19 Hydrogen bonds: B:R.158, B:Q.178 4NC.4: 14 residues within 4Å: Chain C: T.16, G.18, P.19, R.142 Chain D: Y.25, Y.109, Y.148, W.150, R.158, H.161, H.163, Q.178, I.192 Ligands: FE.3 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:Y.148, D:W.150, D:R.158, D:I.192, C:P.19 Hydrogen bonds: D:R.158, D:Q.178 4NC.6: 14 residues within 4Å: Chain E: T.16, G.18, P.19, R.142 Chain F: Y.25, Y.109, Y.148, W.150, R.158, H.161, H.163, Q.178, I.192 Ligands: FE.5 7 PLIP interactions: 6 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:Y.148, F:W.150, F:R.158, F:I.192, E:P.19 Hydrogen bonds: F:R.158, F:Q.178 4NC.8: 14 residues within 4Å: Chain G: T.16, G.18, P.19, R.142 Chain H: Y.25, Y.109, Y.148, W.150, R.158, H.161, H.163, Q.178, I.192 Ligands: FE.7 7 PLIP interactions: 1 interactions with chain G, 6 interactions with chain H Hydrophobic interactions: G:P.19, H:Y.148, H:W.150, H:R.158, H:I.192 Hydrogen bonds: H:R.158, H:Q.178 4NC.10: 14 residues within 4Å: Chain I: T.16, G.18, P.19, R.142 Chain J: Y.25, Y.109, Y.148, W.150, R.158, H.161, H.163, Q.178, I.192 Ligands: FE.9 7 PLIP interactions: 6 interactions with chain J, 1 interactions with chain I Hydrophobic interactions: J:Y.148, J:W.150, J:R.158, J:I.192, I:P.19 Hydrogen bonds: J:R.158, J:Q.178 4NC.12: 14 residues within 4Å: Chain K: T.16, G.18, P.19, R.142 Chain L: Y.25, Y.109, Y.148, W.150, R.158, H.161, H.163, Q.178, I.192 Ligands: FE.11 7 PLIP interactions: 1 interactions with chain K, 6 interactions with chain L Hydrophobic interactions: K:P.19, L:Y.148, L:W.150, L:R.158, L:I.192 Hydrogen bonds: L:R.158, L:Q.178 4NC.14: 14 residues within 4Å: Chain M: T.16, G.18, P.19, R.142 Chain N: Y.25, Y.109, Y.148, W.150, R.158, H.161, H.163, Q.178, I.192 Ligands: FE.13 7 PLIP interactions: 1 interactions with chain M, 6 interactions with chain N Hydrophobic interactions: M:P.19, N:Y.148, N:W.150, N:R.158, N:I.192 Hydrogen bonds: N:R.158, N:Q.178 4NC.16: 14 residues within 4Å: Chain O: T.16, G.18, P.19, R.142 Chain P: Y.25, Y.109, Y.148, W.150, R.158, H.161, H.163, Q.178, I.192 Ligands: FE.15 10 PLIP interactions: 9 interactions with chain P, 1 interactions with chain O Hydrophobic interactions: P:Y.148, P:W.150, P:R.158, P:I.192, O:P.19 Hydrogen bonds: P:Y.109, P:R.158, P:H.161, P:H.161, P:Q.178 4NC.18: 14 residues within 4Å: Chain Q: T.16, G.18, P.19, R.142 Chain R: Y.25, Y.109, Y.148, W.150, R.158, H.161, H.163, Q.178, I.192 Ligands: FE.17 7 PLIP interactions: 6 interactions with chain R, 1 interactions with chain Q Hydrophobic interactions: R:Y.148, R:W.150, R:R.158, R:I.192, Q:P.19 Hydrogen bonds: R:R.158, R:Q.178 4NC.20: 14 residues within 4Å: Chain S: T.16, G.18, P.19, R.142 Chain T: Y.25, Y.109, Y.148, W.150, R.158, H.161, H.163, Q.178, I.192 Ligands: FE.19 7 PLIP interactions: 1 interactions with chain S, 6 interactions with chain T Hydrophobic interactions: S:P.19, T:Y.148, T:W.150, T:R.158, T:I.192 Hydrogen bonds: T:R.158, T:Q.178 4NC.22: 14 residues within 4Å: Chain U: T.16, G.18, P.19, R.142 Chain V: Y.25, Y.109, Y.148, W.150, R.158, H.161, H.163, Q.178, I.192 Ligands: FE.21 7 PLIP interactions: 6 interactions with chain V, 1 interactions with chain U Hydrophobic interactions: V:Y.148, V:W.150, V:R.158, V:I.192, U:P.19 Hydrogen bonds: V:R.158, V:Q.178 4NC.24: 14 residues within 4Å: Chain W: T.16, G.18, P.19, R.142 Chain X: Y.25, Y.109, Y.148, W.150, R.158, H.161, H.163, Q.178, I.192 Ligands: FE.23 7 PLIP interactions: 6 interactions with chain X, 1 interactions with chain W Hydrophobic interactions: X:Y.148, X:W.150, X:R.158, X:I.192, W:P.19 Hydrogen bonds: X:R.158, X:Q.178

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vetting, M.W. et al., Structure of Acinetobacter strain ADP1 protocatechuate 3, 4-dioxygenase at 2.2 A resolution: implications for the mechanism of an intradiol dioxygenase. Biochemistry (2000)

Release Date

2000-08-09

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
A

E
A

G
A

I
A

K
A

M
A

O
A

Q
A

S
A

U
A

W
A

B
B

D
B

F
B

H
B

J
B

L
B

N
B

P
B

R
B

T
B

V
B

X
B

PROTOCATECHUATE 3,4-DIOXYGENASE ALPHA CHAIN

PROTOCATECHUATE 3,4-DIOXYGENASE BETA CHAIN

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