SMTL ID : 3lwz.1

1.65 Angstrom Resolution Crystal Structure of Type II 3-Dehydroquinate Dehydratase (aroQ) from Yersinia pestis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-12-mer

Ligands

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

BME.1: 7 residues within 4Å: Chain A: N.109, V.110, H.111, V.129, C.131 Ligands: GOL.2, BME.15 No protein-ligand interaction detected (PLIP) BME.7: 7 residues within 4Å: Chain B: N.109, V.110, H.111, V.129, C.131 Ligands: GOL.9, BME.55 No protein-ligand interaction detected (PLIP) BME.11: 7 residues within 4Å: Chain C: N.109, V.110, H.111, V.129, C.131 Ligands: GOL.13, BME.29 No protein-ligand interaction detected (PLIP) BME.15: 5 residues within 4Å: Chain D: N.109, V.110, H.111, C.131 Ligands: BME.1 No protein-ligand interaction detected (PLIP) BME.23: 7 residues within 4Å: Chain E: N.109, V.110, H.111, V.129, C.131 Ligands: GOL.24, BME.37 No protein-ligand interaction detected (PLIP) BME.29: 7 residues within 4Å: Chain F: N.109, V.110, H.111, V.129, C.131 Ligands: BME.11, GOL.31 No protein-ligand interaction detected (PLIP) BME.33: 7 residues within 4Å: Chain G: N.109, V.110, H.111, V.129, C.131 Ligands: GOL.35, BME.51 No protein-ligand interaction detected (PLIP) BME.37: 5 residues within 4Å: Chain H: N.109, V.110, H.111, C.131 Ligands: BME.23 No protein-ligand interaction detected (PLIP) BME.45: 7 residues within 4Å: Chain I: N.109, V.110, H.111, V.129, C.131 Ligands: GOL.46, BME.59 No protein-ligand interaction detected (PLIP) BME.51: 7 residues within 4Å: Chain J: N.109, V.110, H.111, V.129, C.131 Ligands: BME.33, GOL.53 No protein-ligand interaction detected (PLIP) BME.55: 7 residues within 4Å: Chain K: N.109, V.110, H.111, V.129, C.131 Ligands: BME.7, GOL.57 No protein-ligand interaction detected (PLIP) BME.59: 5 residues within 4Å: Chain L: N.109, V.110, H.111, C.131 Ligands: BME.45 No protein-ligand interaction detected (PLIP)

51 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 13 residues within 4Å: Chain A: H.86, E.104, H.106, V.110, H.111, R.117, H.118, H.119, S.120, S.123, V.129 Chain D: H.111 Ligands: BME.1 Ligand excluded by PLIP GOL.3: 7 residues within 4Å: Chain A: A.82, A.83, H.86, S.108, V.110, R.113, R.117 Ligand excluded by PLIP GOL.4: 6 residues within 4Å: Chain A: L.95, L.96, Q.99, I.100, P.101, F.102 Ligand excluded by PLIP GOL.5: 7 residues within 4Å: Chain A: R.92, H.119, S.120, Y.121, D.124 Chain C: F.116 Chain D: H.118 Ligand excluded by PLIP GOL.6: 4 residues within 4Å: Chain A: E.114 Chain B: R.92, L.96, I.125 Ligand excluded by PLIP GOL.8: 7 residues within 4Å: Chain B: A.82, A.83, H.86, S.108, V.110, R.113, R.117 Ligand excluded by PLIP GOL.9: 13 residues within 4Å: Chain B: H.86, E.104, H.106, V.110, H.111, R.117, H.118, H.119, S.120, S.123, V.129 Chain K: H.111 Ligands: BME.7 Ligand excluded by PLIP GOL.10: 5 residues within 4Å: Chain B: L.95, Q.99, I.100, P.101, F.102 Ligand excluded by PLIP GOL.12: 7 residues within 4Å: Chain C: A.82, A.83, H.86, S.108, V.110, R.113, R.117 Ligand excluded by PLIP GOL.13: 13 residues within 4Å: Chain C: H.86, E.104, H.106, V.110, H.111, R.117, H.118, H.119, S.120, S.123, V.129 Chain F: H.111 Ligands: BME.11 Ligand excluded by PLIP GOL.14: 7 residues within 4Å: Chain B: F.116 Chain C: R.92, H.119, S.120, Y.121, D.124 Chain F: H.118 Ligand excluded by PLIP GOL.17: 5 residues within 4Å: Chain D: A.82, A.83, H.86, S.108, R.117 Ligand excluded by PLIP GOL.18: 6 residues within 4Å: Chain D: R.92, H.119, S.120, Y.121, D.124 Chain L: F.116 Ligand excluded by PLIP GOL.19: 12 residues within 4Å: Chain A: H.111 Chain D: H.86, E.104, H.106, V.110, H.111, R.117, H.118, H.119, S.120, S.123, V.129 Ligand excluded by PLIP GOL.20: 5 residues within 4Å: Chain D: R.113, E.114 Chain H: R.92, L.96, I.125 Ligand excluded by PLIP GOL.21: 5 residues within 4Å: Chain D: L.95, Q.99, I.100, P.101, F.102 Ligand excluded by PLIP GOL.22: 6 residues within 4Å: Chain D: E.42, A.45, Q.46, V.50, A.51, L.52 Ligand excluded by PLIP GOL.24: 13 residues within 4Å: Chain E: H.86, E.104, H.106, V.110, H.111, R.117, H.118, H.119, S.120, S.123, V.129 Chain H: H.111 Ligands: BME.23 Ligand excluded by PLIP GOL.25: 7 residues within 4Å: Chain E: A.82, A.83, H.86, S.108, V.110, R.113, R.117 Ligand excluded by PLIP GOL.26: 6 residues within 4Å: Chain E: L.95, L.96, Q.99, I.100, P.101, F.102 Ligand excluded by PLIP GOL.27: 7 residues within 4Å: Chain E: R.92, H.119, S.120, Y.121, D.124 Chain G: F.116 Chain H: H.118 Ligand excluded by PLIP GOL.28: 4 residues within 4Å: Chain E: E.114 Chain F: R.92, L.96, I.125 Ligand excluded by PLIP GOL.30: 7 residues within 4Å: Chain F: A.82, A.83, H.86, S.108, V.110, R.113, R.117 Ligand excluded by PLIP GOL.31: 13 residues within 4Å: Chain C: H.111 Chain F: H.86, E.104, H.106, V.110, H.111, R.117, H.118, H.119, S.120, S.123, V.129 Ligands: BME.29 Ligand excluded by PLIP GOL.32: 5 residues within 4Å: Chain F: L.95, Q.99, I.100, P.101, F.102 Ligand excluded by PLIP GOL.34: 7 residues within 4Å: Chain G: A.82, A.83, H.86, S.108, V.110, R.113, R.117 Ligand excluded by PLIP GOL.35: 13 residues within 4Å: Chain G: H.86, E.104, H.106, V.110, H.111, R.117, H.118, H.119, S.120, S.123, V.129 Chain J: H.111 Ligands: BME.33 Ligand excluded by PLIP GOL.36: 7 residues within 4Å: Chain F: F.116 Chain G: R.92, H.119, S.120, Y.121, D.124 Chain J: H.118 Ligand excluded by PLIP GOL.39: 5 residues within 4Å: Chain H: A.82, A.83, H.86, S.108, R.117 Ligand excluded by PLIP GOL.40: 6 residues within 4Å: Chain D: F.116 Chain H: R.92, H.119, S.120, Y.121, D.124 Ligand excluded by PLIP GOL.41: 12 residues within 4Å: Chain E: H.111 Chain H: H.86, E.104, H.106, V.110, H.111, R.117, H.118, H.119, S.120, S.123, V.129 Ligand excluded by PLIP GOL.42: 5 residues within 4Å: Chain H: R.113, E.114 Chain L: R.92, L.96, I.125 Ligand excluded by PLIP GOL.43: 5 residues within 4Å: Chain H: L.95, Q.99, I.100, P.101, F.102 Ligand excluded by PLIP GOL.44: 6 residues within 4Å: Chain H: E.42, A.45, Q.46, V.50, A.51, L.52 Ligand excluded by PLIP GOL.46: 13 residues within 4Å: Chain I: H.86, E.104, H.106, V.110, H.111, R.117, H.118, H.119, S.120, S.123, V.129 Chain L: H.111 Ligands: BME.45 Ligand excluded by PLIP GOL.47: 7 residues within 4Å: Chain I: A.82, A.83, H.86, S.108, V.110, R.113, R.117 Ligand excluded by PLIP GOL.48: 6 residues within 4Å: Chain I: L.95, L.96, Q.99, I.100, P.101, F.102 Ligand excluded by PLIP GOL.49: 7 residues within 4Å: Chain I: R.92, H.119, S.120, Y.121, D.124 Chain K: F.116 Chain L: H.118 Ligand excluded by PLIP GOL.50: 4 residues within 4Å: Chain I: E.114 Chain J: R.92, L.96, I.125 Ligand excluded by PLIP GOL.52: 7 residues within 4Å: Chain J: A.82, A.83, H.86, S.108, V.110, R.113, R.117 Ligand excluded by PLIP GOL.53: 13 residues within 4Å: Chain G: H.111 Chain J: H.86, E.104, H.106, V.110, H.111, R.117, H.118, H.119, S.120, S.123, V.129 Ligands: BME.51 Ligand excluded by PLIP GOL.54: 5 residues within 4Å: Chain J: L.95, Q.99, I.100, P.101, F.102 Ligand excluded by PLIP GOL.56: 7 residues within 4Å: Chain K: A.82, A.83, H.86, S.108, V.110, R.113, R.117 Ligand excluded by PLIP GOL.57: 13 residues within 4Å: Chain B: H.111 Chain K: H.86, E.104, H.106, V.110, H.111, R.117, H.118, H.119, S.120, S.123, V.129 Ligands: BME.55 Ligand excluded by PLIP GOL.58: 7 residues within 4Å: Chain B: H.118 Chain J: F.116 Chain K: R.92, H.119, S.120, Y.121, D.124 Ligand excluded by PLIP GOL.61: 5 residues within 4Å: Chain L: A.82, A.83, H.86, S.108, R.117 Ligand excluded by PLIP GOL.62: 6 residues within 4Å: Chain H: F.116 Chain L: R.92, H.119, S.120, Y.121, D.124 Ligand excluded by PLIP GOL.63: 12 residues within 4Å: Chain I: H.111 Chain L: H.86, E.104, H.106, V.110, H.111, R.117, H.118, H.119, S.120, S.123, V.129 Ligand excluded by PLIP GOL.64: 5 residues within 4Å: Chain D: R.92, L.96, I.125 Chain L: R.113, E.114 Ligand excluded by PLIP GOL.65: 5 residues within 4Å: Chain L: L.95, Q.99, I.100, P.101, F.102 Ligand excluded by PLIP GOL.66: 6 residues within 4Å: Chain L: E.42, A.45, Q.46, V.50, A.51, L.52 Ligand excluded by PLIP

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.16: 4 residues within 4Å: Chain D: L.11, H.54, L.55, S.66 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.66 Water bridges: D:H.54, D:H.54 EDO.38: 4 residues within 4Å: Chain H: L.11, H.54, L.55, S.66 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:S.66 Water bridges: H:H.54, H:H.54 EDO.60: 4 residues within 4Å: Chain L: L.11, H.54, L.55, S.66 3 PLIP interactions: 3 interactions with chain L Hydrogen bonds: L:S.66 Water bridges: L:H.54, L:H.54

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Minasov, G. et al., 1.65 Angstrom Resolution Crystal Structure of Type II 3-Dehydroquinate Dehydratase (aroQ) from Yersinia pestis. TO BE PUBLISHED

Release Date

2010-03-09

Peptides

3-dehydroquinate dehydratase: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

I
A

J
B

K
C

L
D

3-dehydroquinate dehydratase