SMTL ID : 1wpl.1

Crystal structure of the inhibitory form of rat GTP cyclohydrolase I/GFRP complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-10-10-mer

Ligands

10 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: C.121, H.124, C.192 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.121, A:H.124, A:C.192 ZN.5: 4 residues within 4Å: Chain B: C.121, H.123, H.124, C.192 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.121, B:H.124, B:C.192 ZN.8: 4 residues within 4Å: Chain C: C.121, H.123, H.124, C.192 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.121, C:H.124, C:C.192 ZN.11: 4 residues within 4Å: Chain D: C.121, H.123, H.124, C.192 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.121, D:H.124, D:C.192 ZN.14: 4 residues within 4Å: Chain E: C.121, H.123, H.124, C.192 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:C.121, E:H.124, E:C.192 ZN.16: 4 residues within 4Å: Chain F: C.121, H.123, H.124, C.192 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:C.121, F:H.124, F:C.192 ZN.20: 4 residues within 4Å: Chain G: C.121, H.123, H.124, C.192 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:C.121, G:H.124, G:C.192 ZN.23: 4 residues within 4Å: Chain H: C.121, H.123, H.124, C.192 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:C.121, H:H.124, H:C.192 ZN.26: 3 residues within 4Å: Chain I: C.121, H.124, C.192 4 PLIP interactions: 3 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:C.121, I:H.124, I:C.192, H2O.5 ZN.29: 3 residues within 4Å: Chain J: C.121, H.124, C.192 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:C.121, J:H.124, J:C.192

10 x HBI: 7,8-DIHYDROBIOPTERIN(Non-covalent)

HBI.2: 12 residues within 4Å: Chain A: D.107, M.109, L.137, V.213, T.220, E.223 Chain E: S.208, M.210, R.215, R.221 Chain K: Q.9, I.10 9 PLIP interactions: 1 interactions with chain K, 6 interactions with chain E, 2 interactions with chain A Hydrophobic interactions: K:I.10 Hydrogen bonds: E:S.208, E:M.210, E:R.215, E:R.215, E:R.221, E:R.221, A:M.109 Salt bridges: A:E.223 HBI.3: 12 residues within 4Å: Chain A: S.208, M.210, R.215, R.221 Chain B: D.107, M.109, L.137, V.213, T.220, E.223 Chain L: Q.9, I.10 11 PLIP interactions: 1 interactions with chain L, 6 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: L:I.10 Hydrogen bonds: A:S.208, A:M.210, A:R.215, A:R.215, A:R.221, A:R.221, B:M.109 Water bridges: B:T.220, B:T.220 Salt bridges: B:E.223 HBI.6: 12 residues within 4Å: Chain B: S.208, M.210, R.215, R.221 Chain C: D.107, M.109, L.137, V.213, T.220, E.223 Chain M: Q.9, I.10 8 PLIP interactions: 1 interactions with chain M, 5 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: M:I.10 Hydrogen bonds: B:S.208, B:M.210, B:R.215, B:R.221, B:R.221, C:M.109 Salt bridges: C:E.223 HBI.9: 12 residues within 4Å: Chain C: S.208, M.210, R.215, R.221 Chain D: D.107, M.109, L.137, V.213, T.220, E.223 Chain N: Q.9, I.10 9 PLIP interactions: 2 interactions with chain D, 6 interactions with chain C, 1 interactions with chain N Hydrogen bonds: D:M.109, C:S.208, C:M.210, C:R.215, C:R.215, C:R.221, C:R.221 Salt bridges: D:E.223 Hydrophobic interactions: N:I.10 HBI.12: 11 residues within 4Å: Chain D: S.208, M.210, R.215, R.221 Chain E: D.107, M.109, L.137, T.220, E.223 Chain O: Q.9, I.10 9 PLIP interactions: 1 interactions with chain O, 2 interactions with chain E, 6 interactions with chain D Hydrophobic interactions: O:I.10 Hydrogen bonds: E:M.109, D:S.208, D:M.210, D:R.215, D:R.215, D:R.221, D:R.221 Salt bridges: E:E.223 HBI.17: 11 residues within 4Å: Chain F: D.107, M.109, L.137, T.220, E.223 Chain J: S.208, M.210, R.215, R.221 Chain P: Q.9, I.10 9 PLIP interactions: 6 interactions with chain J, 1 interactions with chain P, 2 interactions with chain F Hydrogen bonds: J:S.208, J:M.210, J:R.221, J:R.221, F:M.109 Water bridges: J:R.215, J:R.215 Hydrophobic interactions: P:I.10 Salt bridges: F:E.223 HBI.18: 11 residues within 4Å: Chain F: S.208, M.210, R.215, R.221 Chain G: D.107, M.109, L.137, T.220, E.223 Chain Q: Q.9, I.10 10 PLIP interactions: 6 interactions with chain F, 3 interactions with chain G, 1 interactions with chain Q Hydrogen bonds: F:S.208, F:M.210, F:R.215, F:R.215, F:R.221, F:R.221, G:M.109 Water bridges: G:T.220 Salt bridges: G:E.223 Hydrophobic interactions: Q:I.10 HBI.21: 12 residues within 4Å: Chain G: S.208, M.210, R.215, R.221 Chain H: D.107, M.109, L.137, V.213, T.220, E.223 Chain R: Q.9, I.10 11 PLIP interactions: 6 interactions with chain G, 4 interactions with chain H, 1 interactions with chain R Hydrogen bonds: G:S.208, G:M.210, G:R.221, G:R.221, H:M.109 Water bridges: G:R.215, G:R.215, H:T.220, H:T.220 Salt bridges: H:E.223 Hydrophobic interactions: R:I.10 HBI.24: 12 residues within 4Å: Chain H: S.208, M.210, R.215, R.221 Chain I: D.107, M.109, L.137, V.213, T.220, E.223 Chain S: Q.9, I.10 10 PLIP interactions: 4 interactions with chain I, 5 interactions with chain H, 1 interactions with chain S Hydrogen bonds: I:M.109, H:S.208, H:M.210, H:R.215, H:R.221, H:R.221 Water bridges: I:T.220, I:T.220 Salt bridges: I:E.223 Hydrophobic interactions: S:I.10 HBI.27: 12 residues within 4Å: Chain I: S.208, M.210, R.215, R.221 Chain J: D.107, M.109, L.137, V.213, T.220, E.223 Chain T: Q.9, I.10 13 PLIP interactions: 4 interactions with chain J, 7 interactions with chain I, 2 interactions with chain T Hydrogen bonds: J:M.109, I:S.208, I:M.210, I:R.215, I:R.221, I:R.221 Water bridges: J:T.220, J:T.220, I:R.215, I:R.215, T:Q.9 Salt bridges: J:E.223 Hydrophobic interactions: T:I.10

10 x 3PO: TRIPHOSPHATE(Non-covalent)

3PO.4: 8 residues within 4Å: Chain A: S.146, K.147, R.150 Chain E: H.124, R.196, G.197 Chain F: K.73, R.77 10 PLIP interactions: 2 interactions with chain F, 5 interactions with chain A, 3 interactions with chain E Salt bridges: F:K.73, F:R.77, A:K.147, A:K.147, A:K.147, A:R.150, E:H.124, E:R.196, E:R.196 Hydrogen bonds: A:S.146 3PO.7: 8 residues within 4Å: Chain A: H.124, R.196, G.197 Chain B: S.146, K.147, R.150 Chain J: K.73, R.77 11 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A, 2 interactions with chain J Hydrogen bonds: B:S.146, A:R.196, J:R.77 Salt bridges: B:K.147, B:K.147, B:K.147, B:R.150, A:H.124, A:R.196, J:K.73 Water bridges: A:V.198 3PO.10: 7 residues within 4Å: Chain B: H.124, R.196 Chain C: S.146, K.147, R.150 Chain I: K.73, R.77 10 PLIP interactions: 2 interactions with chain I, 5 interactions with chain C, 3 interactions with chain B Hydrogen bonds: I:R.77, C:S.146, B:R.196 Salt bridges: I:K.73, C:K.147, C:K.147, C:K.147, C:R.150, B:H.124, B:R.196 3PO.13: 8 residues within 4Å: Chain C: H.124, R.196, G.197 Chain D: S.146, K.147, R.150 Chain H: K.73, R.77 13 PLIP interactions: 2 interactions with chain H, 6 interactions with chain D, 5 interactions with chain C Salt bridges: H:K.73, H:R.77, D:K.147, D:K.147, D:K.147, D:R.150, C:H.124, C:R.196 Hydrogen bonds: D:S.146, C:R.196 Water bridges: D:S.146, C:C.192, C:V.198 3PO.15: 7 residues within 4Å: Chain D: H.124, R.196 Chain E: S.146, K.147, R.150 Chain G: K.73, R.77 10 PLIP interactions: 5 interactions with chain E, 2 interactions with chain G, 3 interactions with chain D Hydrogen bonds: E:S.146, G:R.77, D:R.196 Salt bridges: E:K.147, E:K.147, E:K.147, E:R.150, G:K.73, D:H.124, D:R.196 3PO.19: 8 residues within 4Å: Chain A: K.73, R.77 Chain F: S.146, K.147, R.150 Chain J: H.124, R.196, G.197 10 PLIP interactions: 2 interactions with chain A, 3 interactions with chain J, 5 interactions with chain F Salt bridges: A:K.73, A:R.77, J:H.124, J:R.196, F:K.147, F:K.147, F:K.147, F:R.150 Hydrogen bonds: J:R.196, F:S.146 3PO.22: 8 residues within 4Å: Chain E: K.73, R.77 Chain F: H.124, R.196, G.197 Chain G: S.146, K.147, R.150 10 PLIP interactions: 2 interactions with chain E, 2 interactions with chain F, 6 interactions with chain G Hydrogen bonds: E:R.77, G:S.146 Salt bridges: E:K.73, F:H.124, F:R.196, G:K.147, G:K.147, G:K.147, G:R.150 Water bridges: G:S.146 3PO.25: 8 residues within 4Å: Chain D: K.73, R.77 Chain G: H.124, R.196, G.197 Chain H: S.146, K.147, R.150 10 PLIP interactions: 2 interactions with chain D, 3 interactions with chain G, 5 interactions with chain H Salt bridges: D:K.73, D:R.77, G:H.124, G:H.124, G:R.196, H:K.147, H:K.147, H:K.147, H:R.150 Hydrogen bonds: H:S.146 3PO.28: 7 residues within 4Å: Chain C: K.73, R.77 Chain H: H.124, R.196 Chain I: S.146, K.147, R.150 10 PLIP interactions: 3 interactions with chain H, 2 interactions with chain C, 5 interactions with chain I Hydrogen bonds: H:R.196, I:S.146 Salt bridges: H:H.124, H:R.196, C:K.73, C:R.77, I:K.147, I:K.147, I:K.147, I:R.150 3PO.30: 8 residues within 4Å: Chain B: K.73, R.77 Chain I: H.124, R.196, G.197 Chain J: S.146, K.147, R.150 11 PLIP interactions: 2 interactions with chain B, 3 interactions with chain I, 6 interactions with chain J Salt bridges: B:K.73, B:R.77, I:H.124, I:R.196, J:K.147, J:K.147, J:K.147, J:R.150 Hydrogen bonds: I:R.196, J:S.146 Water bridges: J:R.150

10 x NA: SODIUM ION(Non-functional Binders)

NA.31: 5 residues within 4Å: Chain K: T.8, Q.9, R.11, V.14, G.15 3 PLIP interactions: 3 interactions with chain K Hydrogen bonds: K:Q.9, K:R.11, K:G.15 NA.32: 6 residues within 4Å: Chain L: T.8, Q.9, R.11, V.14, G.15, P.16 3 PLIP interactions: 3 interactions with chain L Hydrogen bonds: L:Q.9, L:P.16 Water bridges: L:T.8 NA.33: 6 residues within 4Å: Chain M: T.8, Q.9, R.11, V.14, G.15, P.16 2 PLIP interactions: 2 interactions with chain M Hydrogen bonds: M:Q.9, M:V.14 NA.34: 6 residues within 4Å: Chain N: T.8, Q.9, R.11, V.14, G.15, P.16 2 PLIP interactions: 2 interactions with chain N Hydrogen bonds: N:T.8, N:Q.9 NA.35: 5 residues within 4Å: Chain O: T.8, Q.9, R.11, V.14, G.15 1 PLIP interactions: 1 interactions with chain O Hydrogen bonds: O:G.15 NA.36: 6 residues within 4Å: Chain P: T.8, Q.9, R.11, V.14, G.15, P.16 2 PLIP interactions: 2 interactions with chain P Hydrogen bonds: P:T.8, P:Q.9 NA.37: 5 residues within 4Å: Chain Q: T.8, Q.9, R.11, V.14, G.15 3 PLIP interactions: 3 interactions with chain Q Hydrogen bonds: Q:T.8, Q:Q.9, Q:R.11 NA.38: 6 residues within 4Å: Chain R: T.8, Q.9, R.11, V.14, G.15, P.16 2 PLIP interactions: 2 interactions with chain R Hydrogen bonds: R:Q.9, R:P.16 NA.39: 6 residues within 4Å: Chain S: T.8, Q.9, R.11, V.14, G.15, P.16 1 PLIP interactions: 1 interactions with chain S Hydrogen bonds: S:V.14 NA.40: 5 residues within 4Å: Chain T: T.8, Q.9, R.11, V.14, G.15 1 PLIP interactions: 1 interactions with chain T Hydrogen bonds: T:R.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maita, N. et al., Structural basis of biopterin-induced inhibition of GTP cyclohydrolase I by GFRP, its feedback regulatory protein. J.Biol.Chem. (2004)

Release Date

2004-09-28

Peptides

GTP cyclohydrolase I: ABCDEFGHIJ
GTP cyclohydrolase I feedback regulatory protein: KLMNOPQRST

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

O
O

P
P

Q
Q

R
R

S
S

T
T

GTP cyclohydrolase I

GTP cyclohydrolase I feedback regulatory protein

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