SMTL ID : 5hud.1

Non-covalent complex of and DAHP synthase and chorismate mutase from Corynebacterium glutamicum with bound transition state analog

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

hetero-4-4-mer

Ligands

66 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 3 residues within 4Å: Chain A: T.49, R.173, H.174 Ligand excluded by PLIP GOL.2: 3 residues within 4Å: Chain A: Q.362, E.365, A.366 Ligand excluded by PLIP GOL.10: 8 residues within 4Å: Chain A: P.67, V.70, A.71, R.270, L.271, A.272, L.284 Chain B: E.106 Ligand excluded by PLIP GOL.11: 7 residues within 4Å: Chain B: K.80, P.130, V.131, K.133, A.251, D.252 Ligands: TRP.24 Ligand excluded by PLIP GOL.12: 6 residues within 4Å: Chain A: E.106 Chain B: V.70, A.71, R.270, L.271, L.284 Ligand excluded by PLIP GOL.13: 5 residues within 4Å: Chain B: R.110, K.114, T.201, R.206, W.210 Ligand excluded by PLIP GOL.14: 2 residues within 4Å: Chain B: N.336, F.337 Ligand excluded by PLIP GOL.15: 3 residues within 4Å: Chain B: G.153, P.155 Ligands: GOL.17 Ligand excluded by PLIP GOL.16: 7 residues within 4Å: Chain B: S.307, M.308, I.309, P.335, N.336, E.338, R.341 Ligand excluded by PLIP GOL.17: 5 residues within 4Å: Chain B: T.49, D.148, R.173, H.174 Ligands: GOL.15 Ligand excluded by PLIP GOL.18: 6 residues within 4Å: Chain B: A.44, K.45, Q.46, Q.47, P.48, T.49 Ligand excluded by PLIP GOL.19: 3 residues within 4Å: Chain B: R.145, S.146, R.294 Ligand excluded by PLIP GOL.25: 2 residues within 4Å: Chain C: E.324, A.363 Ligand excluded by PLIP GOL.26: 4 residues within 4Å: Chain C: M.298, E.325, A.328, Y.329 Ligand excluded by PLIP GOL.27: 3 residues within 4Å: Chain C: R.145, S.146 Ligands: GOL.35 Ligand excluded by PLIP GOL.28: 2 residues within 4Å: Chain C: N.336 Ligands: GOL.29 Ligand excluded by PLIP GOL.29: 5 residues within 4Å: Chain C: S.307, N.336, E.338, R.341 Ligands: GOL.28 Ligand excluded by PLIP GOL.30: 1 residues within 4Å: Ligands: PGE.48 Ligand excluded by PLIP GOL.31: 2 residues within 4Å: Chain C: E.276, G.277 Ligand excluded by PLIP GOL.32: 5 residues within 4Å: Chain C: R.212, V.215, A.216, A.228 Ligands: PGE.101 Ligand excluded by PLIP GOL.33: 6 residues within 4Å: Chain C: A.184, N.185 Chain D: I.180, Y.183 Ligands: PGE.48, PGE.51 Ligand excluded by PLIP GOL.34: 3 residues within 4Å: Chain C: T.49, D.148, H.174 Ligand excluded by PLIP GOL.35: 6 residues within 4Å: Chain C: R.145, L.149, D.150, G.151, N.156 Ligands: GOL.27 Ligand excluded by PLIP GOL.36: 8 residues within 4Å: Chain C: V.121, S.208, N.211, R.212, A.228, I.231, D.232, L.235 Ligand excluded by PLIP GOL.37: 4 residues within 4Å: Chain C: S.103, E.425, E.447, R.453 Ligand excluded by PLIP GOL.38: 1 residues within 4Å: Chain C: V.15 Ligand excluded by PLIP GOL.39: 4 residues within 4Å: Chain C: K.114, Q.118, W.210, T.456 Ligand excluded by PLIP GOL.40: 1 residues within 4Å: Chain C: Y.389 Ligand excluded by PLIP GOL.41: 3 residues within 4Å: Chain C: D.252 Chain D: S.198, A.250 Ligand excluded by PLIP GOL.42: 2 residues within 4Å: Chain C: T.273 Ligands: PEG.47 Ligand excluded by PLIP GOL.43: 3 residues within 4Å: Chain C: E.213, N.217 Ligands: GOL.44 Ligand excluded by PLIP GOL.44: 1 residues within 4Å: Ligands: GOL.43 Ligand excluded by PLIP GOL.57: 3 residues within 4Å: Chain D: E.324, A.363 Ligands: PEG.75 Ligand excluded by PLIP GOL.58: 8 residues within 4Å: Chain D: K.45, E.293, R.294, T.295, R.296, G.297, D.300 Ligands: PG4.79 Ligand excluded by PLIP GOL.59: 5 residues within 4Å: Chain D: R.145, S.146, S.147, N.156 Ligands: GOL.60 Ligand excluded by PLIP GOL.60: 6 residues within 4Å: Chain D: S.147, L.149, D.150, G.151, N.156 Ligands: GOL.59 Ligand excluded by PLIP GOL.61: 7 residues within 4Å: Chain C: S.199, R.206, R.249 Chain D: P.72, E.76, E.275 Ligands: PG4.80 Ligand excluded by PLIP GOL.62: 7 residues within 4Å: Chain D: S.307, M.308, I.309, P.335, N.336, E.338, R.341 Ligand excluded by PLIP GOL.63: 5 residues within 4Å: Chain D: K.45, Q.46, R.145, S.146, R.158 Ligand excluded by PLIP GOL.64: 6 residues within 4Å: Chain D: D.96, A.98, S.103, H.108, E.447, R.453 Ligand excluded by PLIP GOL.65: 5 residues within 4Å: Chain D: T.49, D.148, L.149, R.173, H.174 Ligand excluded by PLIP GOL.66: 4 residues within 4Å: Chain D: M.11, T.14, V.15 Ligands: PEG.71 Ligand excluded by PLIP GOL.67: 6 residues within 4Å: Chain D: E.76, K.80, D.252, Y.254 Ligands: GOL.69, PG4.78 Ligand excluded by PLIP GOL.68: 2 residues within 4Å: Chain D: Q.362, A.363 Ligand excluded by PLIP GOL.69: 7 residues within 4Å: Chain D: K.80, K.133, A.251, D.252, Y.254 Ligands: GOL.67, TRP.84 Ligand excluded by PLIP GOL.85: 5 residues within 4Å: Chain E: D.7, L.9, S.10 Chain F: S.49 Ligands: GOL.98 Ligand excluded by PLIP GOL.86: 5 residues within 4Å: Chain E: K.33, K.37 Ligands: GOL.87, PGE.89, PEG.99 Ligand excluded by PLIP GOL.87: 3 residues within 4Å: Chain E: K.37 Ligands: GOL.86, PGE.89 Ligand excluded by PLIP GOL.88: 3 residues within 4Å: Chain E: R.18 Chain F: V.55, T.57 Ligand excluded by PLIP GOL.93: 4 residues within 4Å: Chain E: R.26, K.33 Chain F: E.69 Ligands: PEG.99 Ligand excluded by PLIP GOL.94: 4 residues within 4Å: Chain E: N.22 Chain F: R.58, A.61, Q.65 Ligand excluded by PLIP GOL.95: 8 residues within 4Å: Chain C: Q.402, E.406, R.409 Chain F: R.53, R.86, G.87, K.88, G.90 Ligand excluded by PLIP GOL.96: 2 residues within 4Å: Chain F: E.68 Ligands: GOL.97 Ligand excluded by PLIP GOL.97: 1 residues within 4Å: Ligands: GOL.96 Ligand excluded by PLIP GOL.98: 2 residues within 4Å: Chain F: S.48 Ligands: GOL.85 Ligand excluded by PLIP GOL.103: 5 residues within 4Å: Chain G: D.30, K.33, R.34, K.37 Ligands: PEG.111 Ligand excluded by PLIP GOL.104: 3 residues within 4Å: Chain G: K.37 Ligands: PEG.109, PGE.112 Ligand excluded by PLIP GOL.105: 5 residues within 4Å: Chain G: L.9, S.10 Chain H: S.48, S.49 Ligands: GOL.118 Ligand excluded by PLIP GOL.106: 1 residues within 4Å: Ligands: PGE.112 Ligand excluded by PLIP GOL.107: 3 residues within 4Å: Chain G: R.26, K.33 Chain H: E.69 Ligand excluded by PLIP GOL.108: 5 residues within 4Å: Chain G: R.58, A.61, I.62, Q.65 Chain H: N.22 Ligand excluded by PLIP GOL.114: 10 residues within 4Å: Chain D: Q.402, E.406, R.409, N.472 Chain H: R.53, R.86, G.87, K.88, G.90 Ligands: GOL.116 Ligand excluded by PLIP GOL.115: 4 residues within 4Å: Chain G: N.22 Chain H: R.58, A.61, Q.65 Ligand excluded by PLIP GOL.116: 6 residues within 4Å: Chain H: Q.40, R.53, G.85, R.86, G.87 Ligands: GOL.114 Ligand excluded by PLIP GOL.117: 1 residues within 4Å: Chain H: E.68 Ligand excluded by PLIP GOL.118: 2 residues within 4Å: Chain H: S.48 Ligands: GOL.105 Ligand excluded by PLIP

16 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 8 residues within 4Å: Chain A: E.73, R.194, T.197, A.251, D.252, I.253, Y.254, H.287 Ligand excluded by PLIP PEG.4: 6 residues within 4Å: Chain A: K.80, P.130, V.131, I.132, K.133 Ligands: TRP.9 Ligand excluded by PLIP PEG.20: 8 residues within 4Å: Chain B: E.73, R.194, T.197, A.251, D.252, I.253, Y.254, H.287 Ligand excluded by PLIP PEG.45: 5 residues within 4Å: Chain C: K.80, D.83, A.89, P.130, I.132 Ligand excluded by PLIP PEG.46: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PEG.47: 1 residues within 4Å: Ligands: GOL.42 Ligand excluded by PLIP PEG.70: 4 residues within 4Å: Chain C: P.72 Chain D: G.200, T.201, R.206 Ligand excluded by PLIP PEG.71: 2 residues within 4Å: Chain D: V.15 Ligands: GOL.66 Ligand excluded by PLIP PEG.72: 1 residues within 4Å: Chain D: E.276 Ligand excluded by PLIP PEG.73: 4 residues within 4Å: Chain D: R.212, V.215, A.216, A.228 Ligand excluded by PLIP PEG.74: 5 residues within 4Å: Chain D: Q.79, A.82, F.337, E.338, P.339 Ligand excluded by PLIP PEG.75: 2 residues within 4Å: Chain D: E.324 Ligands: GOL.57 Ligand excluded by PLIP PEG.99: 2 residues within 4Å: Ligands: GOL.86, GOL.93 Ligand excluded by PLIP PEG.109: 6 residues within 4Å: Chain G: K.33, T.36, K.37, Q.40 Chain H: I.70 Ligands: GOL.104 Ligand excluded by PLIP PEG.110: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PEG.111: 2 residues within 4Å: Ligands: GOL.103, PGE.112 Ligand excluded by PLIP

14 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PGE.48: 6 residues within 4Å: Chain C: I.180 Chain D: I.180, R.181 Ligands: GOL.30, GOL.33, PO4.83 No protein-ligand interaction detected (PLIP) PGE.49: 6 residues within 4Å: Chain C: E.106, R.110 Chain D: V.70, A.71, L.271, L.284 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:A.71 PGE.50: 7 residues within 4Å: Chain C: V.70, A.71, R.270, L.271, L.284 Chain D: E.106, R.110 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.71, C:L.271 PGE.51: 5 residues within 4Å: Chain C: F.101, R.181, N.185 Chain D: V.65 Ligands: GOL.33 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:F.101, C:R.181, C:N.185 PGE.52: 1 residues within 4Å: Chain C: W.13 No protein-ligand interaction detected (PLIP) PGE.76: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PGE.77: 1 residues within 4Å: Chain D: H.6 No protein-ligand interaction detected (PLIP) PGE.89: 4 residues within 4Å: Chain E: K.37 Ligands: GOL.86, GOL.87, PGE.90 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:K.37 PGE.90: 1 residues within 4Å: Ligands: PGE.89 No protein-ligand interaction detected (PLIP) PGE.91: 3 residues within 4Å: Chain E: D.30, R.34 Chain F: E.27 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:E.27, E:R.34 PGE.100: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PGE.101: 2 residues within 4Å: Chain F: R.67 Ligands: GOL.32 2 PLIP interactions: 2 interactions with chain F Water bridges: F:R.67, F:R.67 PGE.112: 3 residues within 4Å: Ligands: GOL.104, GOL.106, PEG.111 No protein-ligand interaction detected (PLIP)

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.6: 4 residues within 4Å: Chain A: C.97, H.379, E.421, D.451 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.97, A:H.379, A:E.421, A:D.451, H2O.4 MN.22: 4 residues within 4Å: Chain B: C.97, H.379, E.421, D.451 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:C.97, B:H.379, B:E.421, B:E.421, B:D.451 MN.54: 4 residues within 4Å: Chain C: C.97, H.379, E.421, D.451 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:C.97, C:H.379, C:E.421, C:D.451, H2O.16 MN.81: 4 residues within 4Å: Chain D: C.97, H.379, E.421, D.451 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.97, D:H.379, D:E.421, D:D.451, H2O.22

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.7: 6 residues within 4Å: Chain A: G.292, E.293, R.294, K.316, R.347, H.379 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.293, A:R.294 Water bridges: A:R.294, A:R.294, A:K.316 Salt bridges: A:K.316, A:R.347, A:H.379 PO4.8: 3 residues within 4Å: Chain A: R.145, S.146, R.294 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.146, A:S.146, A:R.294 Salt bridges: A:R.145 PO4.23: 6 residues within 4Å: Chain B: G.292, E.293, R.294, K.316, R.347, H.379 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:E.293 Water bridges: B:W.290, B:K.316, B:K.316 Salt bridges: B:R.294, B:K.316, B:R.347, B:H.379 PO4.55: 6 residues within 4Å: Chain C: G.292, E.293, R.294, K.316, R.347, H.379 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:E.293, C:D.376, C:D.376 Water bridges: C:E.258, C:R.294, C:R.294, C:K.316, C:K.316 Salt bridges: C:R.294, C:K.316, C:R.347, C:H.379 PO4.82: 6 residues within 4Å: Chain D: G.292, E.293, R.294, K.316, R.347, H.379 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:E.293 Water bridges: D:R.294, D:R.294, D:R.294, D:K.316 Salt bridges: D:R.294, D:K.316, D:R.347, D:H.379 PO4.83: 4 residues within 4Å: Chain D: F.101, R.181, N.185 Ligands: PGE.48 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.185, D:N.185 Salt bridges: D:R.181

4 x TRP: TRYPTOPHAN(Non-covalent)

TRP.9: 14 residues within 4Å: Chain A: L.117, A.120, V.121, T.124, K.133, A.202, L.207, S.247, L.248, A.250, A.251 Chain D: A.240, C.241 Ligands: PEG.4 13 PLIP interactions: 11 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:A.120, A:V.121, A:L.207 Hydrogen bonds: A:A.202, A:S.247, W.9, W.9 Water bridges: A:K.133, A:K.133, A:K.133, A:K.133 Salt bridges: A:K.133 pi-Cation interactions: A:K.133 TRP.24: 14 residues within 4Å: Chain B: L.117, A.120, V.121, T.124, K.133, A.202, L.207, S.247, L.248, A.250, A.251 Chain C: A.240, C.241 Ligands: GOL.11 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:L.117, B:A.120, B:L.207 Hydrogen bonds: B:A.202, B:S.247, C:C.241 Water bridges: B:K.133, B:K.133 Salt bridges: B:K.133 TRP.56: 13 residues within 4Å: Chain B: A.240, C.241 Chain C: L.117, A.120, V.121, T.124, K.133, A.202, L.207, S.247, L.248, A.250, A.251 12 PLIP interactions: 10 interactions with chain C, 2 Ligand-Ligand interactions Hydrophobic interactions: C:A.120, C:V.121, C:L.207 Hydrogen bonds: C:A.202, C:S.247, W.56, W.56 Water bridges: C:K.133, C:K.133, C:K.133 Salt bridges: C:K.133 pi-Cation interactions: C:K.133 TRP.84: 14 residues within 4Å: Chain A: A.240, C.241 Chain D: L.117, A.120, V.121, T.124, K.133, A.202, L.207, S.247, L.248, A.250, A.251 Ligands: GOL.69 9 PLIP interactions: 7 interactions with chain D, 2 Ligand-Ligand interactions Hydrophobic interactions: D:A.120, D:L.207 Hydrogen bonds: D:A.202, D:S.247, W.84, W.84 Water bridges: D:K.133 Salt bridges: D:K.133 pi-Cation interactions: D:K.133

5 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.21: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PG4.53: 4 residues within 4Å: Chain C: A.82, F.337, E.338, P.339 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:F.337 Water bridges: C:N.86 PG4.78: 12 residues within 4Å: Chain C: S.198, R.249 Chain D: E.73, E.76, M.190, R.194, T.197, A.251, D.252, I.253, Y.254 Ligands: GOL.67 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.197, D:A.251, D:I.253 PG4.79: 4 residues within 4Å: Chain D: K.45, E.293, R.296 Ligands: GOL.58 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.296 Water bridges: D:Q.46, D:R.296 PG4.80: 11 residues within 4Å: Chain C: R.110, K.114, G.200, T.201, R.206, W.210 Chain D: P.72, T.273, D.274, E.275 Ligands: GOL.61 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:D.274, C:R.206 Water bridges: C:T.201

4 x TSA: 8-HYDROXY-2-OXA-BICYCLO[3.3.1]NON-6-ENE-3,5-DICARBOXYLIC ACID(Non-covalent)

TSA.92: 12 residues within 4Å: Chain E: R.35, S.39, I.42, R.46, L.54, V.55, R.58, E.59, I.62, L.82, R.86 Chain F: R.18 13 PLIP interactions: 12 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: E:R.58, E:E.59, E:R.86 Hydrogen bonds: E:S.39, E:R.46, E:R.46, E:V.55, E:V.55 Water bridges: E:G.43, E:R.58 Salt bridges: E:R.35, E:R.46, F:R.18 TSA.102: 12 residues within 4Å: Chain E: R.18 Chain F: R.35, S.39, I.42, R.46, L.54, V.55, R.58, E.59, I.62, L.82, R.86 14 PLIP interactions: 13 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:R.58, F:E.59, F:L.82, F:R.86 Hydrogen bonds: F:S.39, F:S.39, F:R.46, F:R.46, F:V.55, F:E.59 Water bridges: F:G.43 Salt bridges: F:R.35, F:R.46, E:R.18 TSA.113: 12 residues within 4Å: Chain G: R.35, S.39, I.42, R.46, L.54, V.55, R.58, E.59, I.62, L.82, R.86 Chain H: R.18 14 PLIP interactions: 13 interactions with chain G, 1 interactions with chain H Hydrophobic interactions: G:R.58, G:E.59, G:R.86 Hydrogen bonds: G:S.39, G:S.39, G:R.46, G:R.46, G:V.55, G:V.55, G:E.59 Water bridges: G:G.43 Salt bridges: G:R.35, G:R.46, H:R.18 TSA.119: 12 residues within 4Å: Chain G: R.18 Chain H: R.35, S.39, I.42, R.46, L.54, V.55, R.58, E.59, I.62, L.82, R.86 14 PLIP interactions: 13 interactions with chain H, 1 interactions with chain G Hydrophobic interactions: H:R.58, H:E.59, H:L.82, H:R.86 Hydrogen bonds: H:S.39, H:R.46, H:R.46, H:V.55, H:V.55 Water bridges: H:G.43, H:R.58 Salt bridges: H:R.35, H:R.46, G:R.18

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Burschowsky, D. et al., Inter-Enzyme Allosteric Regulation of Chorismate Mutase in Corynebacterium glutamicum: Structural Basis of Feedback Activation by Trp. Biochemistry (2018)

Release Date

2017-08-02

Peptides

3-Deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase: ABCD
Chorismate mutase: EFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

3-Deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase

Chorismate mutase

Related Entries With Identical Sequence