SMTL ID : 3lou.1 (2 other biounits)

Crystal structure of Formyltetrahydrofolate deformylase (YP_105254.1) from BURKHOLDERIA MALLEI ATCC 23344 at 1.90 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

1 x UNL: UNKNOWN LIGAND

UNL.1: 9 residues within 4Å: Chain A: L.177, Q.182, V.183, L.184, N.198, H.229, V.231, T.232, D.236 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:L.184, A:S.189, A:T.232, A:D.236, A:D.236, A:D.236 Water bridges: A:H.229, A:E.237

12 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 3 residues within 4Å: Chain A: R.247 Chain B: V.244, R.271 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Water bridges: A:R.247, A:R.247, A:R.247 Salt bridges: A:R.247, B:R.271 SO4.3: 6 residues within 4Å: Chain A: L.105, R.179, H.201, Y.213, L.258, R.262 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.179, A:R.179 Salt bridges: A:R.179, A:H.201, A:R.262 SO4.4: 4 residues within 4Å: Chain A: V.244, R.271 Chain B: R.247 Ligands: EDO.14 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Water bridges: B:R.247, A:V.245, A:R.271, A:R.271 Salt bridges: B:R.247, A:R.271 SO4.5: 5 residues within 4Å: Chain A: S.103, N.131, H.132, M.181, Q.182 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.103, A:S.103, A:N.131, A:Q.182 Water bridges: A:K.104 Salt bridges: A:H.132 SO4.15: 6 residues within 4Å: Chain B: L.105, R.179, H.201, Y.213, L.258, R.262 6 PLIP interactions: 6 interactions with chain B Water bridges: B:R.179, B:Y.213, B:Y.213 Salt bridges: B:R.179, B:H.201, B:R.262 SO4.16: 5 residues within 4Å: Chain B: S.103, N.131, H.132, M.181, Q.182 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.103, B:N.131, B:Q.182 Water bridges: B:K.104 Salt bridges: B:H.132 SO4.25: 6 residues within 4Å: Chain C: L.105, R.179, H.201, Y.213, L.258, R.262 6 PLIP interactions: 6 interactions with chain C Water bridges: C:R.179, C:R.179, C:H.201 Salt bridges: C:R.179, C:H.201, C:R.262 SO4.26: 3 residues within 4Å: Chain C: V.244, R.271 Chain D: R.247 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Water bridges: D:R.247, D:R.247 Salt bridges: D:R.247, C:R.271 SO4.27: 6 residues within 4Å: Chain C: S.103, K.104, N.131, H.132, M.181, Q.182 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:S.103, C:N.131, C:Q.182 Water bridges: C:K.104 Salt bridges: C:K.104, C:H.132 SO4.34: 3 residues within 4Å: Chain C: R.247 Chain D: V.244, R.271 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Water bridges: C:R.247, C:R.247 Salt bridges: C:R.247, D:R.271 SO4.35: 6 residues within 4Å: Chain D: L.105, R.179, H.201, Y.213, L.258, R.262 5 PLIP interactions: 5 interactions with chain D Water bridges: D:R.179, D:R.179 Salt bridges: D:R.179, D:H.201, D:R.262 SO4.36: 5 residues within 4Å: Chain D: S.103, N.131, H.132, M.181, Q.182 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.103, D:S.103, D:N.131, D:Q.182 Water bridges: D:K.104 Salt bridges: D:H.132

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

EDO.6: 2 residues within 4Å: Chain A: R.95, W.116 Ligand excluded by PLIP EDO.7: 7 residues within 4Å: Chain A: T.14, L.15, S.16, Q.86, W.87, A.88 Ligands: EDO.8 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: T.14, R.279, R.280, V.281 Ligands: EDO.7 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: E.40, R.55, V.57, V.92, E.278 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain A: M.118, G.119, K.122 Ligand excluded by PLIP EDO.11: 8 residues within 4Å: Chain A: A.110, L.113, F.114, K.117, H.142 Chain C: F.114, K.117 Ligands: EDO.31 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: D.111, F.114, R.115 Chain C: D.111, F.114, R.115 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain A: R.115, E.120, I.267, A.270, R.271, K.274 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: V.244, V.245, E.246, I.267, R.271 Ligands: SO4.4 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain A: H.250 Chain B: T.42, V.43, F.44, F.291 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain B: S.251, Y.252, Q.256 Ligand excluded by PLIP EDO.23: 2 residues within 4Å: Chain B: H.148, P.150 Ligand excluded by PLIP EDO.24: 2 residues within 4Å: Chain B: R.95, W.116 Ligand excluded by PLIP EDO.29: 5 residues within 4Å: Chain C: T.14, R.279, R.280, V.281 Ligands: EDO.33 Ligand excluded by PLIP EDO.30: 6 residues within 4Å: Chain C: H.90, A.94, R.95, P.96, E.173, R.279 Ligand excluded by PLIP EDO.31: 8 residues within 4Å: Chain A: F.114, K.117 Chain C: A.110, L.113, F.114, K.117, H.142 Ligands: EDO.11 Ligand excluded by PLIP EDO.32: 3 residues within 4Å: Chain C: R.33, H.34, E.75 Ligand excluded by PLIP EDO.33: 8 residues within 4Å: Chain C: T.14, L.15, S.16, Q.86, W.87, A.88, F.282 Ligands: EDO.29 Ligand excluded by PLIP EDO.39: 3 residues within 4Å: Chain D: R.95, W.116, K.117 Ligand excluded by PLIP EDO.40: 4 residues within 4Å: Chain D: Y.180, Q.182, L.184 Ligands: EDO.42 Ligand excluded by PLIP EDO.41: 4 residues within 4Å: Chain D: N.194, F.276, V.281, L.283 Ligand excluded by PLIP EDO.42: 5 residues within 4Å: Chain D: N.198, H.229, V.231, E.237 Ligands: EDO.40 Ligand excluded by PLIP EDO.43: 3 residues within 4Å: Chain D: E.246, V.264, I.267 Ligand excluded by PLIP

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

PEG.17: 6 residues within 4Å: Chain B: K.211, P.212, Y.213, H.214, P.254, E.255 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.211, B:Y.213, B:H.214 PEG.18: 6 residues within 4Å: Chain B: K.117, Q.141, H.142 Chain D: K.117, Q.141, H.142 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Water bridges: D:Q.141, B:K.117 PEG.19: 1 residues within 4Å: Chain B: R.33 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.33 Water bridges: B:G.29, B:R.35 PEG.20: 8 residues within 4Å: Chain B: V.12, E.40, R.55, V.57, V.92, I.277, E.278, R.279 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.40, B:R.55, B:R.55 Water bridges: B:D.91, B:R.279 PEG.28: 6 residues within 4Å: Chain C: E.40, R.55, V.57, V.92, I.277, E.278 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.40, C:R.55, C:R.55 PEG.37: 7 residues within 4Å: Chain C: H.250 Chain D: T.42, V.43, F.44, V.290, F.291, Q.292 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:V.43, D:Q.292 Water bridges: D:V.43, D:Q.292, D:Q.292, D:Q.292 PEG.38: 6 residues within 4Å: Chain D: K.211, P.212, Y.213, H.214, P.254, E.255 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.211, D:Y.213

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of Formyltetrahydrofolate deformylase (YP_105254.1) from BURKHOLDERIA MALLEI ATCC 23344 at 1.90 A resolution. To be published

Release Date

2010-02-23

Peptides

Formyltetrahydrofolate deformylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Formyltetrahydrofolate deformylase

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