SMTL ID : 5k8p.1

Zn2+/Tetrahedral intermediate-bound R289A 5-nitroanthranilate aminohydrolase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-octamer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.86, N.124, E.158, E.196, R.373 Ligands: 6R8.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.86, A:E.196, A:E.196 ZN.4: 5 residues within 4Å: Chain B: H.86, N.124, E.158, E.196 Ligands: 6R8.5 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.86, B:E.196, B:E.196 ZN.7: 4 residues within 4Å: Chain C: H.86, N.124, E.196 Ligands: 6R8.8 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.86, C:E.196, C:E.196 ZN.10: 4 residues within 4Å: Chain D: H.86, N.124, E.158, E.196 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.86, D:E.196, D:E.196 ZN.12: 6 residues within 4Å: Chain E: H.86, N.124, E.158, E.196, R.373 Ligands: 6R8.13 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.86, E:E.196, E:E.196, H2O.36 ZN.15: 4 residues within 4Å: Chain F: H.86, N.124, E.158, E.196 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:H.86, F:E.196, F:E.196 ZN.17: 6 residues within 4Å: Chain G: H.86, N.124, E.158, E.196, R.373 Ligands: 6R8.18 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:H.86, G:E.196, G:E.196 ZN.20: 6 residues within 4Å: Chain H: H.86, N.124, E.158, E.196, R.373 Ligands: 6R8.21 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:H.86, H:E.196, H:E.196

6 x 6R8: (6~{R})-6-azanyl-3-nitro-6-oxidanyl-cyclohexa-1,3-diene-1-carboxylic acid(Non-covalent)

6R8.2: 14 residues within 4Å: Chain A: H.86, I.90, N.124, E.158, D.160, E.196, M.371, W.372, R.373, A.394, G.395 Chain B: Y.223, Y.288 Ligands: ZN.1 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:N.124, A:N.124, B:Y.223 Salt bridges: A:R.373 Hydrophobic interactions: B:Y.223, B:Y.223 6R8.5: 12 residues within 4Å: Chain A: Y.223, Y.288 Chain B: H.86, I.90, N.124, E.158, D.160, E.196, M.371, W.372, R.373 Ligands: ZN.4 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:Y.223, A:Y.223 Hydrogen bonds: A:Y.223, A:Y.223, B:N.124, B:N.124, B:R.373, B:G.395 Salt bridges: B:R.373 6R8.8: 13 residues within 4Å: Chain C: H.86, I.90, N.124, E.158, D.160, E.196, M.371, W.372, R.373, A.394 Chain F: Y.223, Y.288 Ligands: ZN.7 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain F Hydrogen bonds: C:N.124, C:N.124, C:N.124, C:E.158, C:R.373, F:Y.223 Salt bridges: C:R.373 Hydrophobic interactions: F:Y.223, F:Y.223 6R8.13: 14 residues within 4Å: Chain D: Y.223, Y.288 Chain E: H.86, I.90, N.124, E.158, I.159, D.160, E.196, M.371, W.372, R.373, G.395 Ligands: ZN.12 6 PLIP interactions: 3 interactions with chain E, 3 interactions with chain D Hydrophobic interactions: E:I.159, D:Y.223, D:Y.223 Hydrogen bonds: E:N.124, D:Y.223 Salt bridges: E:R.373 6R8.18: 13 residues within 4Å: Chain G: H.86, I.90, N.124, E.158, D.160, E.196, M.371, W.372, R.373, A.394 Chain H: Y.223, Y.288 Ligands: ZN.17 8 PLIP interactions: 5 interactions with chain G, 3 interactions with chain H Hydrogen bonds: G:N.124, G:N.124, G:E.158, G:R.373, H:Y.223 Salt bridges: G:R.373 Hydrophobic interactions: H:Y.223, H:Y.223 6R8.21: 15 residues within 4Å: Chain G: Y.223, Y.288 Chain H: H.86, I.90, N.124, E.158, I.159, D.160, E.196, M.371, W.372, R.373, A.394, G.395 Ligands: ZN.20 8 PLIP interactions: 4 interactions with chain H, 4 interactions with chain G Hydrophobic interactions: H:I.159, G:Y.223, G:Y.223, G:Y.223 Hydrogen bonds: H:R.373, H:A.394, G:Y.223 Salt bridges: H:R.373

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: P.304, D.305, T.306, N.307, F.333, R.335 Chain C: L.381 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:P.304, A:D.305, A:D.305, A:R.335, C:L.381 Water bridges: A:G.336 GOL.6: 8 residues within 4Å: Chain B: P.304, D.305, T.306, N.307, P.308, F.333, R.335 Chain G: L.381 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain G Hydrogen bonds: B:D.305, B:R.335 Water bridges: B:N.307, B:R.335, B:G.336, G:L.381 GOL.9: 7 residues within 4Å: Chain A: L.381, G.382 Chain C: P.304, D.305, T.306, N.307, R.335 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.335, C:R.335 Water bridges: C:D.305, C:N.307, C:N.307, C:G.336 GOL.11: 8 residues within 4Å: Chain D: P.304, D.305, T.306, N.307, P.308, R.335 Chain H: L.381, G.382 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.335, D:R.335 Water bridges: D:N.307, D:N.307, D:G.336 GOL.14: 7 residues within 4Å: Chain E: P.304, D.305, T.306, N.307, P.308, F.333, R.335 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:D.305, E:R.335, E:R.335 Water bridges: E:N.307, E:G.336 GOL.16: 5 residues within 4Å: Chain F: P.304, D.305, T.306, N.307, R.335 5 PLIP interactions: 1 interactions with chain E, 4 interactions with chain F Hydrogen bonds: E:L.381, F:P.304, F:R.335 Water bridges: F:N.307, F:R.335 GOL.19: 7 residues within 4Å: Chain B: L.381 Chain G: P.304, D.305, T.306, N.307, P.308, R.335 7 PLIP interactions: 1 interactions with chain B, 6 interactions with chain G Water bridges: B:G.382, G:N.307, G:N.307, G:G.336 Hydrogen bonds: G:D.305, G:R.335, G:R.335 GOL.22: 5 residues within 4Å: Chain H: P.304, D.305, T.306, N.307, R.335 6 PLIP interactions: 5 interactions with chain H, 1 interactions with chain D Hydrogen bonds: H:P.304, H:R.335, D:G.382 Water bridges: H:N.307, H:N.307, H:G.336

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kalyoncu, S. et al., Enzymatic hydrolysis by transition-metal-dependent nucleophilic aromatic substitution. Nat.Chem.Biol. (2016)

Release Date

2016-10-05

Peptides

5-nitroanthranilic acid aminohydrolase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

5-nitroanthranilic acid aminohydrolase