SMTL ID : 4du6.1

Crystal structure of GTP cyclohydrolase I from Yersinia pestis complexed with GTP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

homo-10-mer

Ligands

10 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.1: 21 residues within 4Å: Chain A: T.89, V.133, I.134, G.135, L.136, S.137, K.138, R.141 Chain B: C.112, H.114, H.115, V.152, Q.153, E.154, H.181, C.183, V.184, R.187, G.188 Chain H: R.67 Ligands: CA.7 24 PLIP interactions: 12 interactions with chain A, 11 interactions with chain B, 1 interactions with chain H Hydrogen bonds: A:I.134, A:L.136, A:S.137, A:S.137, A:S.137, A:K.138, B:H.114, B:Q.153, B:H.181 Water bridges: A:I.134, A:S.137, B:R.187, B:I.189 Salt bridges: A:K.138, A:K.138, A:K.138, A:R.141, B:H.115, B:H.115, B:E.154, B:R.187, B:R.187, H:R.67 pi-Stacking: B:H.114 GTP.6: 21 residues within 4Å: Chain B: T.89, V.133, I.134, G.135, L.136, S.137, K.138, R.141 Chain C: C.112, H.114, H.115, V.152, Q.153, E.154, H.181, V.184, R.187, G.188 Chain G: R.66, R.67 Ligands: CA.11 25 PLIP interactions: 12 interactions with chain B, 11 interactions with chain C, 2 interactions with chain G Hydrogen bonds: B:I.134, B:L.136, B:S.137, B:S.137, B:S.137, B:K.138, C:H.114, C:Q.153, G:R.66 Water bridges: B:I.134, B:S.137, C:R.187, C:I.189 Salt bridges: B:K.138, B:K.138, B:K.138, B:R.141, C:H.115, C:H.115, C:H.115, C:E.154, C:R.187, C:R.187, G:R.67 pi-Stacking: C:H.114 GTP.9: 22 residues within 4Å: Chain C: K.87, T.89, V.133, I.134, G.135, L.136, S.137, K.138, R.141 Chain D: C.112, H.114, H.115, V.152, Q.153, E.154, H.181, C.183, V.184, R.187, G.188 Chain F: R.67 Ligands: CA.17 27 PLIP interactions: 10 interactions with chain D, 16 interactions with chain C, 1 interactions with chain F Hydrogen bonds: D:H.114, D:Q.153, C:I.134, C:L.136, C:S.137, C:S.137, C:S.137, C:S.137, C:S.137, C:K.138 Water bridges: D:R.187, D:R.187, D:R.187, C:I.134 Salt bridges: D:H.115, D:H.115, D:E.154, D:R.187, D:R.187, C:K.87, C:K.87, C:K.87, C:K.138, C:K.138, C:K.138, C:R.141, F:R.67 GTP.15: 19 residues within 4Å: Chain D: T.89, V.133, I.134, G.135, L.136, S.137, K.138, R.141 Chain E: H.114, H.115, V.152, Q.153, E.154, H.181, C.183, V.184, R.187, G.188 Chain J: R.67 22 PLIP interactions: 12 interactions with chain D, 8 interactions with chain E, 2 interactions with chain J Hydrogen bonds: D:I.134, D:L.136, D:S.137, D:S.137, D:S.137, D:S.137, D:S.137, D:K.138, E:Q.153 Salt bridges: D:K.138, D:K.138, D:K.138, D:R.141, E:H.115, E:H.115, E:E.154, E:R.187, E:R.187, J:R.67, J:K.70 Water bridges: E:I.189 pi-Stacking: E:H.114 GTP.19: 20 residues within 4Å: Chain A: C.112, H.114, H.115, V.152, Q.153, E.154, H.181, C.183, V.184, R.187, G.188 Chain E: T.89, V.133, I.134, G.135, L.136, S.137, K.138, R.141 Chain I: R.67 26 PLIP interactions: 12 interactions with chain A, 12 interactions with chain E, 2 interactions with chain I Hydrogen bonds: A:Q.153, A:E.154, A:C.183, E:I.134, E:L.136, E:S.137, E:S.137, E:S.137, E:S.137, E:K.138, I:R.66 Water bridges: A:E.113, A:H.115, A:R.187, A:I.189, E:I.134 Salt bridges: A:H.115, A:E.154, A:R.187, A:R.187, E:K.138, E:K.138, E:K.138, E:R.141, I:R.67 pi-Stacking: A:H.114 GTP.20: 21 residues within 4Å: Chain C: R.67 Chain F: T.89, V.133, I.134, G.135, L.136, S.137, K.138, R.141 Chain G: C.112, H.114, H.115, V.152, Q.153, E.154, H.181, C.183, V.184, R.187, G.188 Ligands: CA.26 23 PLIP interactions: 13 interactions with chain F, 9 interactions with chain G, 1 interactions with chain C Hydrogen bonds: F:T.89, F:I.134, F:L.136, F:S.137, F:S.137, F:S.137, F:K.138, G:Q.153 Water bridges: F:I.134, F:S.137, G:R.187, G:I.189 Salt bridges: F:K.138, F:K.138, F:K.138, F:R.141, G:H.115, G:H.115, G:E.154, G:R.187, G:R.187, C:R.67 pi-Stacking: G:H.114 GTP.25: 21 residues within 4Å: Chain B: R.66, R.67 Chain G: T.89, V.133, I.134, G.135, L.136, S.137, K.138, R.141 Chain H: C.112, H.114, H.115, V.152, Q.153, E.154, H.181, V.184, R.187, G.188 Ligands: CA.30 26 PLIP interactions: 13 interactions with chain G, 11 interactions with chain H, 2 interactions with chain B Hydrogen bonds: G:T.89, G:I.134, G:L.136, G:S.137, G:S.137, G:S.137, G:K.138, H:Q.153, H:H.181, B:R.66 Water bridges: G:I.134, G:S.137, H:R.187, H:I.189 Salt bridges: G:K.138, G:K.138, G:K.138, G:R.141, H:H.115, H:H.115, H:H.115, H:E.154, H:R.187, H:R.187, B:R.67 pi-Stacking: H:H.114 GTP.28: 22 residues within 4Å: Chain A: R.67 Chain H: K.87, T.89, V.133, I.134, G.135, L.136, S.137, K.138, R.141 Chain I: C.112, H.114, H.115, V.152, Q.153, E.154, H.181, C.183, V.184, R.187, G.188 Ligands: CA.36 28 PLIP interactions: 17 interactions with chain H, 10 interactions with chain I, 1 interactions with chain A Hydrogen bonds: H:T.89, H:I.134, H:L.136, H:S.137, H:S.137, H:S.137, H:S.137, H:S.137, H:K.138, I:Q.153, I:H.181 Water bridges: H:I.134, I:R.187, I:R.187, I:R.187 Salt bridges: H:K.87, H:K.87, H:K.87, H:K.138, H:K.138, H:K.138, H:R.141, I:H.115, I:H.115, I:E.154, I:R.187, I:R.187, A:R.67 GTP.34: 19 residues within 4Å: Chain E: R.67 Chain I: T.89, V.133, I.134, G.135, L.136, S.137, K.138, R.141 Chain J: H.114, H.115, V.152, Q.153, E.154, H.181, C.183, V.184, R.187, G.188 25 PLIP interactions: 13 interactions with chain I, 10 interactions with chain J, 2 interactions with chain E Hydrogen bonds: I:T.89, I:I.134, I:L.136, I:S.137, I:S.137, I:S.137, I:S.137, I:S.137, I:K.138, J:H.114, J:Q.153, J:H.181 Salt bridges: I:K.138, I:K.138, I:K.138, I:R.141, J:H.115, J:H.115, J:E.154, J:R.187, J:R.187, E:R.67, E:K.70 Water bridges: J:I.189 pi-Stacking: J:H.114 GTP.38: 20 residues within 4Å: Chain D: R.67 Chain F: C.112, H.114, H.115, V.152, Q.153, E.154, H.181, C.183, V.184, R.187, G.188 Chain J: T.89, V.133, I.134, G.135, L.136, S.137, K.138, R.141 28 PLIP interactions: 13 interactions with chain J, 13 interactions with chain F, 2 interactions with chain D Hydrogen bonds: J:T.89, J:I.134, J:L.136, J:S.137, J:S.137, J:S.137, J:S.137, J:K.138, F:H.114, F:Q.153, F:H.181, F:C.183, D:R.66 Water bridges: J:I.134, F:E.113, F:H.115, F:R.187, F:I.189 Salt bridges: J:K.138, J:K.138, J:K.138, J:R.141, F:H.115, F:E.154, F:R.187, F:R.187, D:R.67 pi-Stacking: F:H.114

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: Q.158, L.161, S.200, L.201, K.206 Chain E: K.96, D.98, E.99 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:Q.158, A:L.201, A:K.206, E:D.98 Water bridges: A:Q.165 GOL.3: 9 residues within 4Å: Chain A: K.96, D.98, E.99 Chain B: Q.158, L.161, S.200, L.201, K.206 Ligands: PEG.4 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:D.98, B:R.21, B:Q.158, B:L.201, B:K.206 Water bridges: A:D.98, A:E.99, B:R.21 GOL.8: 8 residues within 4Å: Chain B: K.96, D.98, E.99 Chain C: Q.158, L.161, S.200, L.201, K.206 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:Q.158, C:L.201, C:L.201, C:K.206, B:K.96 Water bridges: C:R.21, C:R.21 GOL.12: 4 residues within 4Å: Chain C: R.40, H.44, E.47 Chain G: H.44 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.40, C:R.40 GOL.13: 7 residues within 4Å: Chain B: R.104 Chain C: D.120, K.122, D.178, A.179, V.180, A.195 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:D.120, C:D.178, B:R.104 GOL.14: 9 residues within 4Å: Chain C: K.96, D.98, E.99 Chain D: R.21, Q.158, L.161, S.200, L.201, K.206 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:R.21, D:Q.158, D:L.201, D:K.206, C:K.96 GOL.18: 8 residues within 4Å: Chain D: K.96, D.98, E.99 Chain E: Q.158, L.161, S.200, L.201, K.206 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:R.21, E:Q.158, E:L.201, E:K.206, D:D.98 GOL.21: 8 residues within 4Å: Chain F: Q.158, L.161, S.200, L.201, K.206 Chain J: K.96, D.98, E.99 5 PLIP interactions: 4 interactions with chain F, 1 interactions with chain J Hydrogen bonds: F:Q.158, F:L.201, F:K.206, J:D.98 Water bridges: F:Q.165 GOL.22: 9 residues within 4Å: Chain F: K.96, D.98, E.99 Chain G: Q.158, L.161, S.200, L.201, K.206 Ligands: PEG.23 8 PLIP interactions: 5 interactions with chain G, 3 interactions with chain F Hydrogen bonds: G:R.21, G:Q.158, G:L.201, G:K.206, F:D.98 Water bridges: G:R.21, F:D.98, F:E.99 GOL.27: 8 residues within 4Å: Chain G: K.96, D.98, E.99 Chain H: Q.158, L.161, S.200, L.201, K.206 7 PLIP interactions: 6 interactions with chain H, 1 interactions with chain G Hydrogen bonds: H:Q.158, H:L.201, H:L.201, H:K.206, G:K.96 Water bridges: H:R.21, H:R.21 GOL.31: 4 residues within 4Å: Chain B: H.44 Chain H: R.40, H.44, E.47 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:R.40, H:R.40 GOL.32: 7 residues within 4Å: Chain G: R.104 Chain H: D.120, K.122, D.178, A.179, V.180, A.195 3 PLIP interactions: 1 interactions with chain G, 2 interactions with chain H Hydrogen bonds: G:R.104, H:D.120, H:D.178 GOL.33: 9 residues within 4Å: Chain H: K.96, D.98, E.99 Chain I: R.21, Q.158, L.161, S.200, L.201, K.206 6 PLIP interactions: 4 interactions with chain I, 2 interactions with chain H Hydrogen bonds: I:R.21, I:Q.158, I:L.201, I:K.206, H:K.96, H:E.99 GOL.37: 8 residues within 4Å: Chain I: K.96, D.98, E.99 Chain J: Q.158, L.161, S.200, L.201, K.206 5 PLIP interactions: 4 interactions with chain J, 1 interactions with chain I Hydrogen bonds: J:R.21, J:Q.158, J:L.201, J:K.206, I:D.98

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

PEG.4: 9 residues within 4Å: Chain B: R.21, L.23, Q.158, L.161, L.162, Q.165, G.202, G.203 Ligands: GOL.3 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.21, B:R.21, B:L.162, B:Q.165, B:G.203 PEG.23: 9 residues within 4Å: Chain G: R.21, L.23, Q.158, L.161, L.162, Q.165, G.202, G.203 Ligands: GOL.22 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:R.21, G:R.21, G:L.162, G:Q.165, G:G.203

6 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.5: 4 residues within 4Å: Chain B: H.15, L.19, L.27, K.29 1 PLIP interactions: 1 interactions with chain B Water bridges: B:L.27 TRS.10: 5 residues within 4Å: Chain C: H.15, L.19, E.24, L.27, K.29 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:L.27, C:K.29, C:K.29 Water bridges: C:H.15, C:L.27, C:L.27 TRS.16: 5 residues within 4Å: Chain D: H.15, L.19, L.27, R.28, K.29 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:H.15, D:K.29 TRS.24: 4 residues within 4Å: Chain G: H.15, L.19, L.27, K.29 1 PLIP interactions: 1 interactions with chain G Water bridges: G:L.27 TRS.29: 5 residues within 4Å: Chain H: H.15, L.19, E.24, L.27, K.29 5 PLIP interactions: 5 interactions with chain H Hydrogen bonds: H:L.27, H:K.29, H:K.29 Water bridges: H:L.27, H:L.27 TRS.35: 5 residues within 4Å: Chain I: H.15, L.19, L.27, R.28, K.29 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:H.15, I:K.29

6 x CA: CALCIUM ION(Non-covalent)

CA.7: 5 residues within 4Å: Chain B: C.112, H.114, H.115, C.183 Ligands: GTP.1 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.115 CA.11: 5 residues within 4Å: Chain C: C.112, H.114, H.115, C.183 Ligands: GTP.6 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.115 CA.17: 5 residues within 4Å: Chain D: C.112, H.114, H.115, C.183 Ligands: GTP.9 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:H.115 CA.26: 5 residues within 4Å: Chain G: C.112, H.114, H.115, C.183 Ligands: GTP.20 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:H.115 CA.30: 5 residues within 4Å: Chain H: C.112, H.114, H.115, C.183 Ligands: GTP.25 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:H.115 CA.36: 5 residues within 4Å: Chain I: C.112, H.114, H.115, C.183 Ligands: GTP.28 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:H.115

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maltseva, N. et al., Crystal structure of GTP cyclohydrolase I from Yersinia pestis complexed with GTP. To be Published

Release Date

2012-03-21

Peptides

GTP cyclohydrolase 1: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
A

G
B

H
C

I
D

J
E

GTP cyclohydrolase 1