SMTL ID : 2ae8.1

Crystal Structure of Imidazoleglycerol-phosphate Dehydratase from Staphylococcus aureus subsp. aureus N315

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

homo-24-mer

Ligands

64 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: H.65, H.187, E.191 Chain S: H.92 Ligands: MG.51 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain S Metal complexes: A:H.65, A:H.187, A:E.191, S:H.92 MG.2: 4 residues within 4Å: Chain A: H.91, E.95 Chain M: H.188 Ligands: MG.3 6 PLIP interactions: 1 interactions with chain M, 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: M:H.188, A:H.91, A:E.95, H2O.2, H2O.6, H2O.79 MG.3: 4 residues within 4Å: Chain M: M.125, E.191 Ligands: MG.2, MG.33 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain B: H.91, E.95 Chain U: H.188 6 PLIP interactions: 1 interactions with chain U, 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: U:H.188, B:H.91, B:E.95, H2O.7, H2O.12, H2O.13 MG.5: 3 residues within 4Å: Chain B: H.188 Chain F: H.91, E.95 6 PLIP interactions: 1 interactions with chain B, 2 interactions with chain F, 3 Ligand-Water interactions Metal complexes: B:H.188, F:H.91, F:E.95, H2O.34, H2O.36, H2O.36 MG.6: 5 residues within 4Å: Chain B: P.140, Y.141, I.170 Chain S: R.166, I.170 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:P.140, H2O.7, H2O.113 MG.7: 4 residues within 4Å: Chain B: H.65, H.187, E.191 Chain F: H.92 5 PLIP interactions: 1 interactions with chain F, 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: F:H.92, B:H.65, B:H.187, B:E.191, H2O.12 MG.8: 4 residues within 4Å: Chain C: H.65, H.187, E.191 Chain N: H.92 4 PLIP interactions: 1 interactions with chain N, 3 interactions with chain C Metal complexes: N:H.92, C:H.65, C:H.187, C:E.191 MG.9: 4 residues within 4Å: Chain C: H.91, E.95, E.163 Chain D: H.188 6 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: C:H.91, C:E.95, D:H.188, H2O.13, H2O.18, H2O.18 MG.10: 4 residues within 4Å: Chain C: H.92 Chain D: H.65, H.187, E.191 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Metal complexes: D:H.65, D:H.187, D:E.191, C:H.92 MG.11: 5 residues within 4Å: Chain C: N.185, H.187 Chain N: H.91, E.159, L.160 3 PLIP interactions: 2 interactions with chain N, 1 Ligand-Water interactions Metal complexes: N:H.91, N:E.159, H2O.81 MG.12: 3 residues within 4Å: Chain F: H.188 Chain V: H.91, E.95 6 PLIP interactions: 2 interactions with chain V, 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: V:H.91, V:E.95, F:H.188, H2O.32, H2O.33, H2O.133 MG.13: 4 residues within 4Å: Chain E: H.65, H.187, E.191 Chain Q: H.92 5 PLIP interactions: 3 interactions with chain E, 1 interactions with chain Q, 1 Ligand-Water interactions Metal complexes: E:H.65, E:H.187, E:E.191, Q:H.92, H2O.31 MG.14: 3 residues within 4Å: Chain E: H.91, E.95 Chain W: H.188 6 PLIP interactions: 2 interactions with chain E, 1 interactions with chain W, 3 Ligand-Water interactions Metal complexes: E:H.91, E:E.95, W:H.188, H2O.31, H2O.31, H2O.31 MG.15: 3 residues within 4Å: Chain E: E.163, R.166 Chain W: E.127 3 PLIP interactions: 1 interactions with chain W, 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: W:E.127, E:E.163, H2O.27 MG.16: 4 residues within 4Å: Chain F: H.65, H.187, E.191 Chain V: H.92 4 PLIP interactions: 1 interactions with chain V, 3 interactions with chain F Metal complexes: V:H.92, F:H.65, F:H.187, F:E.191 MG.17: 5 residues within 4Å: Chain G: H.65, H.187, E.191 Chain M: H.92 Ligands: MG.35 4 PLIP interactions: 3 interactions with chain G, 1 interactions with chain M Metal complexes: G:H.65, G:H.187, G:E.191, M:H.92 MG.18: 4 residues within 4Å: Chain G: H.91, E.95 Chain S: H.188 Ligands: MG.19 6 PLIP interactions: 1 interactions with chain S, 2 interactions with chain G, 3 Ligand-Water interactions Metal complexes: S:H.188, G:H.91, G:E.95, H2O.39, H2O.43, H2O.116 MG.19: 4 residues within 4Å: Chain S: M.125, E.191 Ligands: MG.18, MG.49 No protein-ligand interaction detected (PLIP) MG.20: 3 residues within 4Å: Chain H: H.91, E.95 Chain O: H.188 6 PLIP interactions: 2 interactions with chain H, 1 interactions with chain O, 3 Ligand-Water interactions Metal complexes: H:H.91, H:E.95, O:H.188, H2O.43, H2O.49, H2O.49 MG.21: 3 residues within 4Å: Chain H: H.188 Chain L: H.91, E.95 6 PLIP interactions: 1 interactions with chain H, 2 interactions with chain L, 3 Ligand-Water interactions Metal complexes: H:H.188, L:H.91, L:E.95, H2O.70, H2O.73, H2O.73 MG.22: 5 residues within 4Å: Chain H: P.140, Y.141, I.170 Chain M: R.166, I.170 3 PLIP interactions: 1 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:P.140, H2O.43, H2O.76 MG.23: 4 residues within 4Å: Chain H: H.65, H.187, E.191 Chain L: H.92 5 PLIP interactions: 3 interactions with chain H, 1 interactions with chain L, 1 Ligand-Water interactions Metal complexes: H:H.65, H:H.187, H:E.191, L:H.92, H2O.49 MG.24: 4 residues within 4Å: Chain I: H.65, H.187, E.191 Chain T: H.92 4 PLIP interactions: 3 interactions with chain I, 1 interactions with chain T Metal complexes: I:H.65, I:H.187, I:E.191, T:H.92 MG.25: 4 residues within 4Å: Chain I: H.91, E.95, E.163 Chain J: H.188 6 PLIP interactions: 2 interactions with chain I, 1 interactions with chain J, 3 Ligand-Water interactions Metal complexes: I:H.91, I:E.95, J:H.188, H2O.50, H2O.54, H2O.55 MG.26: 4 residues within 4Å: Chain I: H.92 Chain J: H.65, H.187, E.191 4 PLIP interactions: 3 interactions with chain J, 1 interactions with chain I Metal complexes: J:H.65, J:H.187, J:E.191, I:H.92 MG.27: 5 residues within 4Å: Chain I: N.185, H.187 Chain T: H.91, E.159, L.160 3 PLIP interactions: 2 interactions with chain T, 1 Ligand-Water interactions Metal complexes: T:H.91, T:E.159, H2O.117 MG.28: 3 residues within 4Å: Chain L: H.188 Chain P: H.91, E.95 6 PLIP interactions: 2 interactions with chain P, 1 interactions with chain L, 3 Ligand-Water interactions Metal complexes: P:H.91, P:E.95, L:H.188, H2O.69, H2O.70, H2O.96 MG.29: 4 residues within 4Å: Chain K: H.65, H.187, E.191 Chain W: H.92 5 PLIP interactions: 3 interactions with chain K, 1 interactions with chain W, 1 Ligand-Water interactions Metal complexes: K:H.65, K:H.187, K:E.191, W:H.92, H2O.67 MG.30: 3 residues within 4Å: Chain K: H.91, E.95 Chain Q: H.188 6 PLIP interactions: 2 interactions with chain K, 1 interactions with chain Q, 3 Ligand-Water interactions Metal complexes: K:H.91, K:E.95, Q:H.188, H2O.67, H2O.67, H2O.67 MG.31: 3 residues within 4Å: Chain K: E.163, R.166 Chain Q: E.127 3 PLIP interactions: 1 interactions with chain Q, 1 interactions with chain K, 1 Ligand-Water interactions Metal complexes: Q:E.127, K:E.163, H2O.63 MG.32: 4 residues within 4Å: Chain L: H.65, H.187, E.191 Chain P: H.92 4 PLIP interactions: 1 interactions with chain P, 3 interactions with chain L Metal complexes: P:H.92, L:H.65, L:H.187, L:E.191 MG.33: 5 residues within 4Å: Chain A: H.92 Chain M: H.65, H.187, E.191 Ligands: MG.3 4 PLIP interactions: 3 interactions with chain M, 1 interactions with chain A Metal complexes: M:H.65, M:H.187, M:E.191, A:H.92 MG.34: 4 residues within 4Å: Chain G: H.188 Chain M: H.91, E.95 Ligands: MG.35 6 PLIP interactions: 2 interactions with chain M, 1 interactions with chain G, 3 Ligand-Water interactions Metal complexes: M:H.91, M:E.95, G:H.188, H2O.43, H2O.75, H2O.79 MG.35: 4 residues within 4Å: Chain G: M.125, E.191 Ligands: MG.17, MG.34 No protein-ligand interaction detected (PLIP) MG.36: 3 residues within 4Å: Chain C: H.188 Chain N: H.91, E.95 6 PLIP interactions: 2 interactions with chain N, 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: N:H.91, N:E.95, C:H.188, H2O.80, H2O.85, H2O.85 MG.37: 3 residues within 4Å: Chain N: H.188 Chain R: H.91, E.95 6 PLIP interactions: 2 interactions with chain R, 1 interactions with chain N, 3 Ligand-Water interactions Metal complexes: R:H.91, R:E.95, N:H.188, H2O.107, H2O.109, H2O.109 MG.38: 5 residues within 4Å: Chain A: R.166, I.170 Chain N: P.140, Y.141, I.170 3 PLIP interactions: 1 interactions with chain N, 2 Ligand-Water interactions Metal complexes: N:P.140, H2O.3, H2O.79 MG.39: 4 residues within 4Å: Chain N: H.65, H.187, E.191 Chain R: H.92 5 PLIP interactions: 3 interactions with chain N, 1 interactions with chain R, 1 Ligand-Water interactions Metal complexes: N:H.65, N:H.187, N:E.191, R:H.92, H2O.85 MG.40: 4 residues within 4Å: Chain H: H.92 Chain O: H.65, H.187, E.191 4 PLIP interactions: 3 interactions with chain O, 1 interactions with chain H Metal complexes: O:H.65, O:H.187, O:E.191, H:H.92 MG.41: 4 residues within 4Å: Chain O: H.91, E.95, E.163 Chain P: H.188 6 PLIP interactions: 2 interactions with chain O, 1 interactions with chain P, 3 Ligand-Water interactions Metal complexes: O:H.91, O:E.95, P:H.188, H2O.86, H2O.91, H2O.91 MG.42: 4 residues within 4Å: Chain O: H.92 Chain P: H.65, H.187, E.191 4 PLIP interactions: 3 interactions with chain P, 1 interactions with chain O Metal complexes: P:H.65, P:H.187, P:E.191, O:H.92 MG.43: 5 residues within 4Å: Chain H: H.91, E.159, L.160 Chain O: N.185, H.187 3 PLIP interactions: 2 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:H.91, H:E.159, H2O.44 MG.44: 3 residues within 4Å: Chain D: H.91, E.95 Chain R: H.188 6 PLIP interactions: 1 interactions with chain R, 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: R:H.188, D:H.91, D:E.95, H2O.23, H2O.105, H2O.106 MG.45: 4 residues within 4Å: Chain K: H.92 Chain Q: H.65, H.187, E.191 5 PLIP interactions: 3 interactions with chain Q, 1 interactions with chain K, 1 Ligand-Water interactions Metal complexes: Q:H.65, Q:H.187, Q:E.191, K:H.92, H2O.104 MG.46: 3 residues within 4Å: Chain E: H.188 Chain Q: H.91, E.95 6 PLIP interactions: 1 interactions with chain E, 2 interactions with chain Q, 3 Ligand-Water interactions Metal complexes: E:H.188, Q:H.91, Q:E.95, H2O.104, H2O.104, H2O.104 MG.47: 3 residues within 4Å: Chain E: E.127 Chain Q: E.163, R.166 3 PLIP interactions: 1 interactions with chain Q, 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: Q:E.163, E:E.127, H2O.100 MG.48: 4 residues within 4Å: Chain D: H.92 Chain R: H.65, H.187, E.191 4 PLIP interactions: 3 interactions with chain R, 1 interactions with chain D Metal complexes: R:H.65, R:H.187, R:E.191, D:H.92 MG.49: 5 residues within 4Å: Chain G: H.92 Chain S: H.65, H.187, E.191 Ligands: MG.19 4 PLIP interactions: 3 interactions with chain S, 1 interactions with chain G Metal complexes: S:H.65, S:H.187, S:E.191, G:H.92 MG.50: 4 residues within 4Å: Chain A: H.188 Chain S: H.91, E.95 Ligands: MG.51 6 PLIP interactions: 2 interactions with chain S, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: S:H.91, S:E.95, A:H.188, H2O.7, H2O.111, H2O.116 MG.51: 4 residues within 4Å: Chain A: M.125, E.191 Ligands: MG.1, MG.50 No protein-ligand interaction detected (PLIP) MG.52: 3 residues within 4Å: Chain I: H.188 Chain T: H.91, E.95 6 PLIP interactions: 2 interactions with chain T, 1 interactions with chain I, 3 Ligand-Water interactions Metal complexes: T:H.91, T:E.95, I:H.188, H2O.116, H2O.121, H2O.122 MG.53: 3 residues within 4Å: Chain T: H.188 Chain X: H.91, E.95 6 PLIP interactions: 1 interactions with chain T, 2 interactions with chain X, 3 Ligand-Water interactions Metal complexes: T:H.188, X:H.91, X:E.95, H2O.143, H2O.145, H2O.146 MG.54: 5 residues within 4Å: Chain G: R.166, I.170 Chain T: P.140, Y.141, I.170 3 PLIP interactions: 1 interactions with chain T, 2 Ligand-Water interactions Metal complexes: T:P.140, H2O.40, H2O.116 MG.55: 4 residues within 4Å: Chain T: H.65, H.187, E.191 Chain X: H.92 5 PLIP interactions: 1 interactions with chain X, 3 interactions with chain T, 1 Ligand-Water interactions Metal complexes: X:H.92, T:H.65, T:H.187, T:E.191, H2O.122 MG.56: 4 residues within 4Å: Chain B: H.92 Chain U: H.65, H.187, E.191 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain U Metal complexes: B:H.92, U:H.65, U:H.187, U:E.191 MG.57: 4 residues within 4Å: Chain U: H.91, E.95, E.163 Chain V: H.188 6 PLIP interactions: 1 interactions with chain V, 2 interactions with chain U, 3 Ligand-Water interactions Metal complexes: V:H.188, U:H.91, U:E.95, H2O.123, H2O.127, H2O.128 MG.58: 4 residues within 4Å: Chain U: H.92 Chain V: H.65, H.187, E.191 4 PLIP interactions: 3 interactions with chain V, 1 interactions with chain U Metal complexes: V:H.65, V:H.187, V:E.191, U:H.92 MG.59: 5 residues within 4Å: Chain B: H.91, E.159, L.160 Chain U: N.185, H.187 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.91, B:E.159, H2O.8 MG.60: 3 residues within 4Å: Chain J: H.91, E.95 Chain X: H.188 6 PLIP interactions: 1 interactions with chain X, 2 interactions with chain J, 3 Ligand-Water interactions Metal complexes: X:H.188, J:H.91, J:E.95, H2O.60, H2O.142, H2O.142 MG.61: 4 residues within 4Å: Chain E: H.92 Chain W: H.65, H.187, E.191 5 PLIP interactions: 3 interactions with chain W, 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: W:H.65, W:H.187, W:E.191, E:H.92, H2O.140 MG.62: 3 residues within 4Å: Chain K: H.188 Chain W: H.91, E.95 6 PLIP interactions: 1 interactions with chain K, 2 interactions with chain W, 3 Ligand-Water interactions Metal complexes: K:H.188, W:H.91, W:E.95, H2O.140, H2O.140, H2O.140 MG.63: 3 residues within 4Å: Chain K: E.127 Chain W: E.163, R.166 3 PLIP interactions: 1 interactions with chain W, 1 interactions with chain K, 1 Ligand-Water interactions Metal complexes: W:E.163, K:E.127, H2O.136 MG.64: 4 residues within 4Å: Chain J: H.92 Chain X: H.65, H.187, E.191 4 PLIP interactions: 3 interactions with chain X, 1 interactions with chain J Metal complexes: X:H.65, X:H.187, X:E.191, J:H.92

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., Crystal Structure of Imidazoleglycerol-phosphate Dehydratase from Staphylococcus aureus subsp. aureus N315. To be Published

Release Date

2005-09-06

Peptides

Imidazoleglycerol-phosphate dehydratase: ABCDEFGHIJKLMNOPQRSTUVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
A

H
B

I
C

J
D

K
E

L
F

M
A

N
B

O
C

P
D

Q
E

R
F

S
A

T
B

U
C

V
D

W
E

X
F

Imidazoleglycerol-phosphate dehydratase