SMTL ID : 7alb.2 (1 other biounit)

human GCH-GFRP stimulatory complex 7-deaza-GTP bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

hetero-10-10-mer

Ligands

10 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.100, H.103, C.171 Ligands: QBQ.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.100, A:H.103, A:C.171, H2O.1 ZN.4: 4 residues within 4Å: Chain B: C.100, H.103, C.171 Ligands: QBQ.5 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.100, B:H.103, B:C.171 ZN.6: 4 residues within 4Å: Chain C: C.100, H.103, C.171 Ligands: QBQ.7 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.100, C:H.103, C:C.171 ZN.8: 4 residues within 4Å: Chain D: C.100, H.103, C.171 Ligands: QBQ.10 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.100, D:H.103, D:C.171, H2O.5 ZN.9: 4 residues within 4Å: Chain E: C.100, H.103, C.171 Ligands: QBQ.2 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:C.100, E:H.103, E:C.171, H2O.6 ZN.11: 4 residues within 4Å: Chain F: C.100, H.103, C.171 Ligands: QBQ.14 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:C.100, F:H.103, F:C.171, H2O.7 ZN.13: 4 residues within 4Å: Chain G: C.100, H.103, C.171 Ligands: QBQ.16 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:C.100, G:H.103, G:C.171 ZN.15: 4 residues within 4Å: Chain H: C.100, H.103, C.171 Ligands: QBQ.18 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:C.100, H:H.103, H:C.171 ZN.17: 4 residues within 4Å: Chain I: C.100, H.103, C.171 Ligands: QBQ.20 4 PLIP interactions: 3 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:C.100, I:H.103, I:C.171, H2O.10 ZN.19: 4 residues within 4Å: Chain J: C.100, H.103, C.171 Ligands: QBQ.12 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:C.100, J:H.103, J:C.171

10 x QBQ: 7-deaza-GTP(Non-covalent)

QBQ.2: 20 residues within 4Å: Chain A: N.77, A.79, F.81, V.121, L.122, G.123, L.124, S.125, K.126, R.129 Chain E: C.100, H.102, H.103, V.140, Q.141, E.142, H.169, R.175 Chain F: R.56 Ligands: ZN.9 23 PLIP interactions: 1 interactions with chain F, 14 interactions with chain A, 8 interactions with chain E Salt bridges: F:R.56, A:K.126, A:K.126, A:K.126, A:R.129, E:H.103, E:H.103, E:E.142, E:R.175, E:R.175 Hydrophobic interactions: A:L.124 Hydrogen bonds: A:N.77, A:L.122, A:L.124, A:S.125, A:S.125, A:S.125, A:K.126, E:Q.141 Water bridges: A:K.126, A:K.126, E:V.177 pi-Cation interactions: E:H.102 QBQ.3: 21 residues within 4Å: Chain A: C.100, H.102, H.103, V.140, Q.141, E.142, H.169, R.175, G.176 Chain B: N.77, A.79, F.81, V.121, L.122, G.123, L.124, S.125, K.126, R.129 Chain J: R.56 Ligands: ZN.1 24 PLIP interactions: 9 interactions with chain A, 14 interactions with chain B, 1 interactions with chain J Hydrogen bonds: A:Q.141, B:N.77, B:L.122, B:L.124, B:S.125, B:S.125, B:S.125, B:K.126, J:R.56 Water bridges: A:E.142, A:V.177, B:K.126, B:K.126 Salt bridges: A:H.103, A:H.103, A:E.142, A:R.175, A:R.175, B:K.126, B:K.126, B:K.126, B:R.129 pi-Stacking: A:H.102 Hydrophobic interactions: B:L.124 QBQ.5: 21 residues within 4Å: Chain B: C.100, H.102, H.103, V.140, Q.141, E.142, H.169, R.175, G.176 Chain C: N.77, A.79, F.81, V.121, L.122, G.123, L.124, S.125, K.126, R.129 Chain I: R.56 Ligands: ZN.4 26 PLIP interactions: 14 interactions with chain C, 11 interactions with chain B, 1 interactions with chain I Hydrophobic interactions: C:L.124, B:V.140 Hydrogen bonds: C:N.77, C:L.122, C:L.124, C:S.125, C:S.125, C:S.125, C:K.126, B:Q.141 Water bridges: C:K.126, C:R.129, B:H.103, B:R.175, B:V.177 Salt bridges: C:K.126, C:K.126, C:K.126, C:R.129, B:H.103, B:H.103, B:E.142, B:R.175, B:R.175, I:R.56 pi-Cation interactions: B:H.102 QBQ.7: 23 residues within 4Å: Chain C: C.100, H.102, H.103, V.140, Q.141, E.142, H.169, C.171, R.175, G.176 Chain D: N.77, A.79, F.81, V.121, L.122, G.123, L.124, S.125, K.126, R.129 Chain H: K.52, R.56 Ligands: ZN.6 20 PLIP interactions: 8 interactions with chain C, 11 interactions with chain D, 1 interactions with chain H Hydrophobic interactions: C:V.140 Hydrogen bonds: C:Q.141, D:N.77, D:L.122, D:L.124, D:S.125, D:S.125, D:S.125, D:K.126, H:R.56 Salt bridges: C:H.103, C:H.103, C:E.142, C:R.175, C:R.175, D:K.126, D:K.126, D:K.126, D:R.129 pi-Cation interactions: C:H.102 QBQ.10: 21 residues within 4Å: Chain D: C.100, H.102, H.103, V.140, Q.141, E.142, H.169, R.175, G.176 Chain E: N.77, A.79, F.81, V.121, L.122, G.123, L.124, S.125, K.126, R.129 Chain G: R.56 Ligands: ZN.8 26 PLIP interactions: 10 interactions with chain D, 15 interactions with chain E, 1 interactions with chain G Hydrophobic interactions: D:V.140, E:L.124 Hydrogen bonds: D:Q.141, E:N.77, E:L.122, E:L.124, E:S.125, E:S.125, E:S.125, E:S.125, E:K.126 Water bridges: D:R.175, D:V.177, E:K.126, E:R.129 Salt bridges: D:H.103, D:H.103, D:E.142, D:R.175, D:R.175, E:K.126, E:K.126, E:K.126, E:R.129, G:R.56 pi-Cation interactions: D:H.102 QBQ.12: 21 residues within 4Å: Chain A: R.56 Chain F: N.77, D.78, F.81, V.121, L.122, G.123, L.124, S.125, K.126, R.129 Chain J: C.100, H.102, H.103, V.140, Q.141, E.142, H.169, C.171, R.175 Ligands: ZN.19 27 PLIP interactions: 16 interactions with chain F, 10 interactions with chain J, 1 interactions with chain A Hydrophobic interactions: F:L.124, J:V.140 Hydrogen bonds: F:N.77, F:L.122, F:L.124, F:S.125, F:S.125, F:S.125, F:S.125, F:K.126, F:K.126, J:Q.141 Water bridges: F:L.122, F:S.125, J:H.103, J:C.171, J:R.175 Salt bridges: F:K.126, F:K.126, F:K.126, F:R.129, J:H.103, J:H.103, J:E.142, J:R.175, J:R.175, A:R.56 QBQ.14: 22 residues within 4Å: Chain E: R.56 Chain F: C.100, H.102, H.103, V.140, Q.141, E.142, H.169, C.171, R.175, G.176 Chain G: N.77, A.79, F.81, V.121, L.122, G.123, L.124, S.125, K.126, R.129 Ligands: ZN.11 26 PLIP interactions: 15 interactions with chain G, 10 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: G:L.124 Hydrogen bonds: G:N.77, G:L.122, G:L.124, G:S.125, G:S.125, G:K.126, G:K.126, F:Q.141, E:R.56 Water bridges: G:K.126, G:R.129, G:R.129, F:C.171, F:C.171, F:R.175 Salt bridges: G:K.126, G:K.126, G:K.126, G:R.129, F:H.103, F:H.103, F:E.142, F:R.175, F:R.175 pi-Cation interactions: F:H.102 QBQ.16: 21 residues within 4Å: Chain D: R.56 Chain G: C.100, H.102, H.103, V.140, Q.141, E.142, H.169, R.175, G.176 Chain H: N.77, A.79, F.81, V.121, L.122, G.123, L.124, S.125, K.126, R.129 Ligands: ZN.13 22 PLIP interactions: 12 interactions with chain H, 10 interactions with chain G Hydrogen bonds: H:N.77, H:L.122, H:L.124, H:S.125, H:S.125, H:S.125, H:S.125, H:K.126, G:Q.141 Salt bridges: H:K.126, H:K.126, H:K.126, H:R.129, G:H.103, G:H.103, G:E.142, G:R.175, G:R.175 Water bridges: G:R.175, G:R.175, G:R.175 pi-Cation interactions: G:H.102 QBQ.18: 21 residues within 4Å: Chain C: R.56 Chain H: C.100, H.102, H.103, V.140, Q.141, E.142, H.169, R.175, G.176 Chain I: N.77, A.79, F.81, V.121, L.122, G.123, L.124, S.125, K.126, R.129 Ligands: ZN.15 25 PLIP interactions: 14 interactions with chain I, 10 interactions with chain H, 1 interactions with chain C Hydrophobic interactions: I:L.124 Hydrogen bonds: I:N.77, I:L.122, I:L.124, I:S.125, I:S.125, I:S.125, I:S.125, I:K.126, I:K.126, H:Q.141 Salt bridges: I:K.126, I:K.126, I:K.126, I:R.129, H:H.103, H:H.103, H:E.142, H:R.175, H:R.175, C:R.56 Water bridges: H:R.175, H:R.175, H:V.177 pi-Stacking: H:H.102 QBQ.20: 21 residues within 4Å: Chain B: R.56 Chain I: C.100, H.102, H.103, V.140, Q.141, E.142, H.169, R.175, G.176 Chain J: N.77, A.79, F.81, V.121, L.122, G.123, L.124, S.125, K.126, R.129 Ligands: ZN.17 24 PLIP interactions: 8 interactions with chain I, 15 interactions with chain J, 1 interactions with chain B Hydrogen bonds: I:Q.141, J:N.77, J:L.122, J:L.124, J:S.125, J:S.125, J:S.125, J:S.125, J:K.126, J:K.126, B:R.56 Water bridges: I:R.175, J:K.126 Salt bridges: I:H.103, I:H.103, I:E.142, I:R.175, I:R.175, J:K.126, J:K.126, J:K.126, J:R.129 pi-Stacking: I:H.102 Hydrophobic interactions: J:L.124

10 x PHE: PHENYLALANINE(Non-covalent)

PHE.21: 12 residues within 4Å: Chain B: E.195, P.197 Chain K: Q.12, I.13, R.14, M.15, Q.78, L.80 Chain L: V.76, G.77, Q.78, T.79 7 PLIP interactions: 3 interactions with chain K, 4 interactions with chain L Hydrophobic interactions: K:L.80, L:V.76 Hydrogen bonds: K:I.13, K:Q.78, L:Q.78, L:T.79, L:T.79 PHE.22: 12 residues within 4Å: Chain C: E.195, P.197 Chain L: Q.12, I.13, R.14, M.15, Q.78, L.80 Chain M: V.76, G.77, Q.78, T.79 7 PLIP interactions: 4 interactions with chain M, 3 interactions with chain L, Hydrophobic interactions: M:V.76, L:L.80 Hydrogen bonds: M:Q.78, M:T.79, M:T.79, L:I.13, L:Q.78 PHE.23: 12 residues within 4Å: Chain D: E.195, P.197 Chain M: Q.12, I.13, R.14, M.15, Q.78, L.80 Chain N: V.76, G.77, Q.78, T.79 9 PLIP interactions: 1 Ligand-Ligand interactions, 3 interactions with chain M, 5 interactions with chain N Water bridges: F.23 Hydrophobic interactions: M:L.80, N:V.76, N:V.76 Hydrogen bonds: M:I.13, M:Q.78, N:Q.78, N:T.79, N:T.79 PHE.24: 12 residues within 4Å: Chain E: E.195, P.197 Chain N: Q.12, I.13, R.14, M.15, Q.78, L.80 Chain O: V.76, G.77, Q.78, T.79 8 PLIP interactions: 3 interactions with chain N, 4 interactions with chain O, 1 Ligand-Ligand interactions Hydrophobic interactions: N:L.80, O:V.76 Hydrogen bonds: N:I.13, N:Q.78, O:Q.78, O:T.79, O:T.79 Water bridges: F.24 PHE.25: 12 residues within 4Å: Chain A: E.195, P.197 Chain K: V.76, G.77, Q.78, T.79 Chain O: Q.12, I.13, R.14, M.15, Q.78, L.80 8 PLIP interactions: 1 Ligand-Ligand interactions, 4 interactions with chain K, 3 interactions with chain O Water bridges: F.25 Hydrophobic interactions: K:V.76, O:L.80 Hydrogen bonds: K:Q.78, K:T.79, K:T.79, O:I.13, O:Q.78 PHE.26: 12 residues within 4Å: Chain G: E.195, P.197 Chain P: Q.12, I.13, R.14, M.15, Q.78, L.80 Chain Q: V.76, G.77, Q.78, T.79 9 PLIP interactions: 3 interactions with chain Q, 4 interactions with chain P, 2 Ligand-Ligand interactions Hydrophobic interactions: Q:V.76, Q:V.76, P:L.80 Hydrogen bonds: Q:Q.78, P:I.13, P:Q.78, P:Q.78, F.26 Water bridges: F.26 PHE.27: 12 residues within 4Å: Chain H: E.195, P.197 Chain Q: Q.12, I.13, R.14, M.15, Q.78, L.80 Chain R: V.76, G.77, Q.78, T.79 7 PLIP interactions: 1 Ligand-Ligand interactions, 4 interactions with chain Q, 2 interactions with chain R Water bridges: F.27 Hydrophobic interactions: Q:L.80, R:V.76 Hydrogen bonds: Q:I.13, Q:Q.78, Q:Q.78, R:Q.78 PHE.28: 12 residues within 4Å: Chain I: E.195, P.197 Chain R: Q.12, I.13, R.14, M.15, Q.78, L.80 Chain S: V.76, G.77, Q.78, T.79 8 PLIP interactions: 3 interactions with chain S, 4 interactions with chain R, 1 Ligand-Ligand interactions Hydrophobic interactions: S:V.76, S:V.76, R:L.80 Hydrogen bonds: S:Q.78, R:I.13, R:Q.78, R:Q.78, F.28 PHE.29: 12 residues within 4Å: Chain J: E.195, P.197 Chain S: Q.12, I.13, R.14, M.15, Q.78, L.80 Chain T: V.76, G.77, Q.78, T.79 8 PLIP interactions: 4 interactions with chain S, 1 Ligand-Ligand interactions, 3 interactions with chain T Hydrophobic interactions: S:L.80, T:V.76, T:V.76 Hydrogen bonds: S:I.13, S:Q.78, S:Q.78, F.29, T:Q.78 PHE.30: 12 residues within 4Å: Chain F: E.195, P.197 Chain P: V.76, G.77, Q.78, T.79 Chain T: Q.12, I.13, R.14, M.15, Q.78, L.80 9 PLIP interactions: 4 interactions with chain T, 3 interactions with chain P, 2 Ligand-Ligand interactions Hydrophobic interactions: T:L.80, P:V.76, P:V.76 Hydrogen bonds: T:I.13, T:Q.78, T:Q.78, P:Q.78, F.30 Water bridges: F.30

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ebenhoch, R. et al., A hybrid approach reveals the allosteric regulation of GTP cyclohydrolase I. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2021-10-13

Peptides

GTP cyclohydrolase 1: ABCDEFGHIJ
GTP cyclohydrolase 1 feedback regulatory protein: KLMNOPQRST

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
K

B
L

C
M

D
N

E
O

F
P

G
Q

H
R

I
S

J
T

K
k

L
l

M
m

N
n

O
o

P
p

Q
q

R
r

S
s

T
t

GTP cyclohydrolase 1

GTP cyclohydrolase 1 feedback regulatory protein

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